---

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	error	path	name	type	comments	error_original	good_original	SMILES	is_name3_too_long	formatting_error
PTR.params	ERROR: unrecognized aa type PTR	ptm-caa/PTR.params	PTR	TYPE POLYMER	rosetta residue topology file residue type APL CB to sidechain heavyatom distance – max observed at residue 74 in ubiquitin	ERROR: unrecognized aa type PTR	False		False
SEP.params	ERROR: unrecognized aa type SEP	ptm-caa/SEP.params	SEP	TYPE POLYMER	rosetta residue topology file residue type APL O to CB distance; max observed in ubiquitin	ERROR: unrecognized aa type SEP	False		False
TPO.params	ERROR: unrecognized aa type TPO	ptm-caa/TPO.params	TPO	TYPE POLYMER	rosetta residue topology file residue type APL O to CB distance; max observed in ubiquitin	ERROR: unrecognized aa type TPO	False		False
B3D.params		beta-peptide/B3D.params	B3D	TYPE POLYMER	rosetta residue topology file residue type APL O to CB distance – max O-CB observed in ubiquitin NCAA_ROTLIB_NUM_ROTAMER_BINS 2 3 3		True	N[C@H](CCO)CC(O)O	False
B3H.params		beta-peptide/B3H.params	B3H	TYPE POLYMER	rosetta residue topology file residue type APL CB to sidechain heavy atom disance – max observed on residue 74 of ubiquitin		True	N[C@H](CCO)CC1CNCN1	False
B3P.params		beta-peptide/B3P.params	B3P	TYPE POLYMER	rosetta residue topology file residue type APL Declare that the NV atom should shadow the N atom to the cart-bonded term. APL O to CB distance; max observed in ubiquitin		True	OCC[C@@H]1CCCN1	False
B3F.params		beta-peptide/B3F.params	B3F	TYPE POLYMER	rosetta residue topology file residue type APL CB to side chain heavyatom distance – max as observed on residue 74 of ubiquitin NCAA_ROTLIB_NUM_ROTAMER_BINS 2 3 2		True	N[C@H](CCO)CC1CCCCC1	False
B3R.params	segfault	beta-peptide/B3R.params	B3R	TYPE POLYMER	rosetta residue topology file residue type APL CB to sidechain heavyatom distance – max observed at residue 74 in ubiquitin		True		False
B3V.params		beta-peptide/B3V.params	B3V	TYPE POLYMER	rosetta residue topology file residue type		True	CC(C)[C@H](N)CCO	False
B3N.params		beta-peptide/B3N.params	B3N	TYPE POLYMER	rosetta residue topology file residue type APL O to CB distance; max observed in ubiquitin		True	N[C@@H](O)C[C@H](N)CCO	False
B3X.params	segfault	beta-peptide/B3X.params	B3X	TYPE POLYMER	rosetta residue topology file residue type APL CB to side chain heavyatom distance – max as observed on residue 74 of ubiquitin		True		False
cisACHC.params	segfault					name	False		False
B3T.params		beta-peptide/B3T.params	B3T	TYPE POLYMER	rosetta residue topology file residue type APL O to CB distance; max observed in ubiquitin		True	C[C@@H](O)[C@H](N)CCO	False
B3L.params		beta-peptide/B3L.params	B3L	TYPE POLYMER	rosetta residue topology file residue type ATOM N Nbb NH1 -0.47 ATOM CA CAbb CT1 0.07 ATOM CM CAbb CT2 -0.18 ATOM C CObb C 0.51 ATOM O OCbb O -0.51 ATOM CB CH2 CT2 -0.18 ATOM CG CH1 CT1 -0.09 ATOM CD1 CH3 CT3 -0.27 ATOM CD2 CH3 CT3 -0.27 ATOM H HNbb H 0.31 ATOM HA Hapo HB 0.09 ATOM 1HB Hapo HA 0.09 ATOM 2HB Hapo HA 0.09 ATOM HG Hapo HA 0.09 ATOM 1HD1 Hapo HA 0.09 ATOM 2HD1 Hapo HA 0.09 ATOM 3HD1 Hapo HA 0.09 ATOM 1HD2 Hapo HA 0.09 ATOM 2HD2 Hapo HA 0.09 ATOM 3HD2 Hapo HA 0.09 ATOM 1HM Hapo HB 0.09 ATOM 2HM Hapo HB 0.09 APL O to CB distance; max observed in ubiquitin		True	CC(C)C[C@H](N)CCO	False
B3Q.params		beta-peptide/B3Q.params	B3Q	TYPE POLYMER	rosetta residue topology file residue type APL CB to sidechain heavyatom distance – max observed at residue 74 in ubiquitin		True	NC1CC[C@@H](CCO)NO1	False
B3E.params		beta-peptide/B3E.params	B3E	TYPE POLYMER	rosetta residue topology file residue type APL CB to furthest side chain heavy atom distance – max as observed from res 74 on ubiquitin		True	OCC[C@@H]1CC[C@H](O)ON1	False
B3I.params		beta-peptide/B3I.params	B3I	TYPE POLYMER	rosetta residue topology file residue type APL O to CB distance; max observed in ubiquitin		True	CC[C@H](C)[C@H](N)CCO	False
cisACPC.params	segfault					name	False		False
B3S.params		beta-peptide/B3S.params	B3S	TYPE POLYMER	rosetta residue topology file residue type APL O to CB distance; max observed in ubiquitin		True	N[C@@H](CO)CCO	False
B3K.params	segfault	beta-peptide/B3K.params	B3K	TYPE POLYMER	rosetta residue topology file residue type APL CB to side chain heavyatom distance – max observed in residue 74 of ubiquitin		True		False
transACPC.params	segfault					name	False		False
B3G.params		beta-peptide/B3G.params	B3G	TYPE POLYMER	rosetta residue topology file We are referring to this beta-amino acid as beta-3-glycine, in analogy to the alpha-amino acids. Confusingly, this is also referred to in the literature as beta-Ala (or 3-amino propanoic acid). residue type APL CA to O distance – not yet measured; default to max CB to O distance		True	NCCCO	False
B3C.params		beta-peptide/B3C.params	B3C	TYPE POLYMER	rosetta residue topology file residue type APL O to CB distance – max O-CB observed in ubiquitin		True	N[C@@H](CS)CCO	False
B3O.params		beta-peptide/B3O.params	B3O	TYPE POLYMER	rosetta residue topology file residue type APL CB to side chain heavyatom distance – max observed in residue 74 of ubiquitin		True	OCC[C@@H]1CCC[NH2+][NH2+]1	False
B3W.params		beta-peptide/B3W.params	B3W	TYPE POLYMER	rosetta residue topology file residue type amw 4/15 changed to gaussian charges ATOM N Nbb NH1 -0.47 ATOM CA CAbb CT1 0.07 ATOM CM CAbb CT2 -0.18 ATOM C CObb C 0.51 ATOM O OCbb O -0.51 ATOM CB CH2 CT2 -0.18 ATOM CG aroC CY -0.03 ATOM CD1 aroC CA 0.035 ATOM CD2 aroC CPT -0.02 ATOM NE1 Ntrp NY -0.61 ATOM CE2 aroC CPT 0.13 ATOM CE3 aroC CA -0.115 ATOM CZ2 aroC CA -0.115 ATOM CZ3 aroC CA -0.115 ATOM CH2 aroC CA -0.115 ATOM H HNbb H 0.31 ATOM HE1 Hpol H 0.38 ATOM HD1 Haro HP 0.115 ATOM HZ2 Haro HP 0.115 ATOM HH2 Haro HP 0.115 ATOM HZ3 Haro HP 0.115 ATOM HE3 Haro HP 0.115 ATOM HA Hapo HB 0.09 ATOM 1HB Hapo HA 0.09 ATOM 2HB Hapo HA 0.09 ATOM 1HM Hapo HB 0.09 ATOM 2HM Hapo HB 0.09 APL CB to sidechain heavyatom distance – max observed at residue 74 in ubiquitin		True	N[C@H](CCO)CC1CNC2CCCCC12	False
B3M.params		beta-peptide/B3M.params	B3M	TYPE POLYMER	rosetta residue topology file residue type APL CB to sidechain heavyatom distance – max observed on residue 74 of ubiquitin		True	OCC[C@@H]1CC[SH]2CN12	False
B3A.params		beta-peptide/B3A.params	B3A	TYPE POLYMER	rosetta residue topology file This is beta-3-homoalanine, also referred to in the literature as 3-aminobutanoic acid (beta-Abu). residue type APL O to CB DISTANCE – MAX O-CB OBSERVED IN UBQ		True	C[C@H](N)CCO	False
B3Y.params		beta-peptide/B3Y.params	B3Y	TYPE POLYMER	rosetta residue topology file residue type APL CB to sidechain heavyatom distance – max observed at residue 74 in ubiquitin		True	N[C@H](CCO)CC1CCC(O)CC1	False
08B.params	segfault					name	False		False
08A.params	segfault					name	False		False
MCY.params	segfault					name	False		False
TFT.params	segfault					name	False		False
TRAD_n.params	segfault					name	False		False
TRCY_n.params	segfault					name	False		False
TRGU_n.params	segfault					name	False		False
TURA_n.params	segfault					name	False		False
URA_s.params	segfault					name	False		False
RAD_n.params	segfault					name	False		False
RCY_n.params	segfault					name	False		False
RGU_s.params	segfault					name	False		False
RGU_n.params	segfault					name	False		False
RCY_s.params	segfault					name	False		False
RAD_s.params	segfault					name	False		False
URA_n.params	segfault					name	False		False
PPU.params	segfault					name	False		False
I6A.params	segfault					name	False		False
1MA.params	segfault					name	False		False
A44.params	segfault					name	False		False
INO.params	segfault					name	False		False
CFM.params	segfault					name	False		False
5IU.params	segfault					name	False		False
1AP.params	segfault					name	False		False
S2C.params	segfault					name	False		False
OMU.params	segfault					name	False		False
OMC.params	segfault					name	False		False
1PU.params	segfault					name	False		False
FA7.params	segfault					name	False		False
BRU.params	segfault					name	False		False
M1I.params	segfault					name	False		False
CNM.params	segfault					name	False		False
7MG.params	ATOM_ALIAS H21 1H2	nucleic/rna_nonnatural/7MG.params	7MG	TYPE POLYMER	Need to correct this – this residue is really supposed to have a nonplanar ring contact amw579@stanford.edu residue type PROTON_CHI 4 SAMPLES 1 -140 EXTRA 1 PROTON_CHI 4 SAMPLES 6 -140 -80 -20 40 100 160 EXTRA 1 15		True		False
6MG.params	segfault					name	False		False
Q.params	segfault					name	False		False
PUR.params	segfault					name	False		False
NPU.params	segfault					name	False		False
IGU.params	segfault					name	False		False
MST.params	segfault					name	False		False
K2C.params	segfault					name	False		False
M2G.params		nucleic/rna_nonnatural/M2G.params	M2G	TYPE POLYMER	Gaussian-corrected charges and positions via HF/6-31G(d), SCF=Tight optimization contact amw579@nyu.edu residue type		True	CN(C)C1NC(O)C2NCN([C@@H]3O[C@H](COP(O)O)[C@@H](O)[C@H]3O)C2N1	False
MTA.params	segfault					name	False		False
OMG.params	segfault					name	False		False
MOT.params	segfault					name	False		False
1MG.params	segfault					name	False		False
yW.params	segfault					name	False		False
31U.params	segfault					name	False		False
PSU.params		nucleic/rna_nonnatural/PSU.params	PSU	TYPE POLYMER	Gaussian corrected charges and positions. via HF/6-31G(d), SCF=Tight optimization contact amw579@nyu.edu residue type ATOM P Phos H 1.632254 ATOM OP2 OOC H -0.872767 ATOM OP1 OOC H -0.777087 ATOM O5’ Oet2 H -0.787763 ATOM C5’ CH2 H 0.019865 ATOM C4’ CH1 H 0.175569 ATOM O4’ Oet3 H -0.702727 ATOM C3’ CH1 H 0.159936 ATOM O3’ Oet2 H -0.759692 ATOM C1’ CH1 H 0.204083 ATOM C2’ CH2 H 0.097770 ATOM O2’ OH H -0.824212 ATOM N1 Ntrp H -0.882369 ATOM C2 CObb H 1.030875 ATOM O2 OCbb H -0.656171 ATOM N3 Ntrp H -0.928441 what am I doing even ATOM C4 CObb H 0.843965 ATOM O4 OCbb H -0.634142 ATOM C5 aroC H -0.300369 ATOM C6 aroC H 0.129864 ATOM H5’ Hapo H 0.153263 ATOM H5’’ Hapo H 0.174148 ATOM H4’ Hapo H 0.168109 ATOM H3’ Hapo H 0.197051 ATOM H2’ Hapo H 0.178952 ATOM HO2’ Hpol H 0.515879 ATOM H1’ Hapo H 0.193856 ATOM H3 Hpol H 0.395142 ATOM H1 Hpol H 0.462676 ATOM H6 Haro H 0.395624 -0.882369 – in URA, -0.34 1.030875 – in URA, 0.51 -0.656171 – in URA, -0.41 -0.928441 – in URA, -0.46 0.843965 – in URA, 0.5 -0.634142 – in URA, -0.45 -0.300369 – in URA, -0.15 0.129864 – in URA, 0.17 0.395142 – in URA, 0.36 0.462676 – in URA, <=> H5, 0.17 0.395624 – in URA, 0.17		True	OC1NCC([C@@H]2O[C@H](COP(O)O)[C@@H](O)[C@H]2O)C(O)N1	False
RIA.params	segfault					name	False		False
MHU.params	segfault					name	False		False
52C.params	segfault					name	False		False
2ST.params	segfault					name	False		False
C43.params	segfault					name	False		False
A2M.params	segfault					name	False		False
CNS.params	segfault					name	False		False
52U.params	segfault					name	False		False
5BU.params	segfault					name	False		False
MIA.params	segfault					name	False		False
5JO.params	segfault					name	False		False
G48.params	segfault					name	False		False
M3G.params	segfault					name	False		False
7DA.params	segfault					name	False		False
OMI.params	segfault					name	False		False
T6A.params	segfault					name	False		False
SRG.params	segfault					name	False		False
FMC.params	segfault					name	False		False
NMT.params	segfault					name	False		False
S4A.params	segfault					name	False		False
M5U.params	segfault					name	False		False
4OC.params	ATOM_ALIAS H41 1H4	nucleic/rna_nonnatural/4OC.params	4OC	TYPE POLYMER	Gauss-corrected via HF/6-31G(d), SCF=Tight optimization contact amw579@nyu.edu residue type BOND VO4’ C1’ virt PROTON_CHI 4 SAMPLES 1 -140 EXTRA 1 PROTON_CHI 4 SAMPLES 6 -140 -80 -20 40 100 160 EXTRA 1 15		True		False
3MC.params	segfault					name	False		False
S4U.params	segfault					name	False		False
MPU.params	segfault					name	False		False
IHA.params	segfault					name	False		False
8OG.params	segfault					name	False		False
U36.params	segfault					name	False		False
O2W.params	segfault					name	False		False
5FC.params	segfault					name	False		False
5FU.params	segfault					name	False		False
UR3.params		nucleic/rna_nonnatural/UR3.params	UR3	TYPE POLYMER	Gaussian corrected charges and positions via HF/6-31G(d), SCF=Tight optimization contact amw579@nyu.edu residue type better atom type!		True	CN1C(O)CCN([C@@H]2O[C@H](COP(O)O)[C@@H](O)[C@H]2O)C1O	False
3TD.params		nucleic/rna_nonnatural/3TD.params	3TD	TYPE POLYMER	AMW optimized contact amw579@stanford.edu residue type This is a stretch – really, it’s two steps removed – UR3 x PSU		True	CN1C(O)CCN([C@@H]2O[C@H](COP(O)O)[C@@H](O)[C@H]2O)C1O	False
CNT.params	segfault					name	False		False
4SU.params	segfault					name	False		False
2AP.params	segfault					name	False		False
F5C.params	segfault					name	False		False
S4C.params	segfault					name	False		False
2MU.params		nucleic/rna_nonnatural/2MU.params	2MU	TYPE POLYMER	Replaced with QM charges and coordinates. Not averaging charges over Hs. Since we don’t do induced charge effects… it makes sense to me to explicitly give the induced charges, then let sampling find that conformation in H optimization. Also did not re-adjust charges after removing the second methylphosphate from optimization. The summed charges are very close to -1 anyway. Didn’t change coordinates of LOWER or associated Os. via HF/6-31G(d), SCF=Tight optimization contact amw579@nyu.edu residue type ATOM VO4’ VIRT VIRT 0.00 BOND VO4’ C1’		True	CO[C@@H]1[C@H](O)[C@@H](COP(O)O)O[C@H]1N1CCC(O)NC1O	False
FMA.params	segfault					name	False		False
SSG.params	segfault					name	False		False
FMU.params	segfault					name	False		False
2MA.params	ATOM_ALIAS H61 1H6	nucleic/rna_nonnatural/2MA.params	2MA	TYPE POLYMER	Now with Gaussian charges and corrected positions via HF/6-31G(d), SCF=Tight optimization contact amw579@nyu.edu residue type BOND VO4’ C1’ PROTON_CHI 4 SAMPLES 1 -140 EXTRA 1 PROTON_CHI 4 SAMPLES 6 -140 -80 -20 40 100 160 EXTRA 1 15		True		False
2FU.params	segfault					name	False		False
2SU.params	segfault					name	False		False
6MZ.params	ATOM_ALIAS H62 2H6	nucleic/rna_nonnatural/6MZ.params	6MZ	TYPE POLYMER	AMW optimized contact amw579@stanford.edu residue type BOND VO4’ C1’ AMW HOW TO SAMPLE CHI 5 N1 C6 N6 C9 PROTON_CHI 5 SAMPLES 2 0 180		True		False
H2U.params	segfault					name	False		False
MOU.params	segfault					name	False		False
SRU.params	segfault					name	False		False
5MU.params	segfault					name	False		False
C5L.params	segfault					name	False		False
C5T.params	segfault					name	False		False
SRA.params	segfault					name	False		False
S4G.params	segfault					name	False		False
SSC.params	segfault					name	False		False
2MG.params	ATOM_ALIAS H21 1H2	nucleic/rna_nonnatural/2MG.params	2MG	TYPE POLYMER	Gaussian corrected charges and locations via HF/6-31G(d), SCF=Tight optimization contact amw579@nyu.edu residue type ATOM VO4’ VIRT VIRT 0.00 BOND VO4’ C1’ PROTON_CHI 4 SAMPLES 1 -140 EXTRA 1 PROTON_CHI 4 SAMPLES 6 -140 -80 -20 40 100 160 EXTRA 1 15		True		False
SSU.params	segfault					name	False		False
SSA.params	segfault					name	False		False
FMG.params	segfault					name	False		False
SRC.params	segfault					name	False		False
5MC.params	ATOM_ALIAS H41 1H4	nucleic/rna_nonnatural/5MC.params	5MC	TYPE POLYMER	Gaussian charges and positions via HF/6-31G(d), SCF=Tight optimization contact amw579@nyu.edu residue type Why isn’t this CH1? BOND VO4’ C1’ PROTON_CHI 4 SAMPLES 1 -140 EXTRA 1 PROTON_CHI 4 SAMPLES 6 -140 -80 -20 40 100 160 EXTRA 1 15		True		False
NST.params	segfault					name	False		False
CMT.params	segfault					name	False		False
OAU.params	segfault					name	False		False
ICY.params	segfault					name	False		False
APU.params	segfault					name	False		False
G7M.params	ATOM_ALIAS H21 1H2	nucleic/rna_nonnatural/G7M.params	G7M	TYPE POLYMER	Gaussian corrected charges and positions via HF/6-31G(d), SCF=Tight optimization contact amw579@stanford.edu residue type PROTON_CHI 4 SAMPLES 1 -140 EXTRA 1 PROTON_CHI 4 SAMPLES 6 -140 -80 -20 40 100 160 EXTRA 1 15		True		False
A4C.params	segfault					name	False		False
M26.params	segfault					name	False		False
THY.params	segfault					name	False		False
GNP.params		nucleic/dna/GNP.params	GNP	TYPE LIGAND			True	NC1NC(O)C2NCN([C@@H]3O[C@H](CO[PH](O)(O)O[PH](O)(O)N[PH](O)(O)O)[C@@H](O)[C@H]3O)C2N1	False
GDP.params		nucleic/dna/GDP.params	GDP	TYPE LIGAND			True	N[C@H]1NC2C(NCN2[C@@H]2O[C@H](CO[PH](O)(O)O[PH](O)(O)O)[C@@H](O)[C@H]2O)[C@H](O)N1	False
GUA.params	segfault					name	False		False
GTP.params		nucleic/dna/GTP.params	GTP	TYPE LIGAND			True	N[C@H]1NC(O)C2NCN([C@@H]3O[C@H](CO[PH](O)(O)O[PH](O)(O)O[PH](O)(O)O)[C@@H](O)[C@H]3O)C2N1	False
ADE.params	segfault					name	False		False
CYT.params	segfault					name	False		False
RCY.params	segfault					name	False		False
URA.params	segfault					name	False		False
RGU.params	segfault					name	False		False
TYR_D.params	segfault					name	False		False
GLU_P1.params	segfault					name	False		False
ASP_P1.params	segfault					name	False		False
LYS_D.params	segfault					name	False		False
ASP_P2.params	segfault					name	False		False
GLU_P2.params	segfault					name	False		False
HIS_P.params	segfault					name	False		False
PWAT_V.params	segfault					name	False		False
PWAT.params	segfault					name	False		False
HOH_V.params	segfault					name	False		False
TP5.params	segfault					name	False		False
TP3.params	segfault					name	False		False
HOH.params		water/HOH.params	HOH	TYPE LIGAND	This used to be a direct copy of TP3.params but is now modified for use with Frank and Ryan’s solvation methods, giving the water its own atom types for parameterization with the beta-nov16 ff Did not want to use the TP3 residue type, since TP3 implies a particular set of parameters and liquid behavior that is not matched here This residue type can be converted to a virtual residue by the packer (effectively “packing” for water occupancy or lack of occupancy). hack – max distance from hbond anchor atom to farthest O position, since packing assumes that NBR_ATOM doesnt move during packing which is not true with repackable position waters… need a better solution for this		True	O	False
OU3_ASN.params	segfault					name	False		False
OU3_TYR.params	segfault					name	False		False
OU3_VAL.params	segfault					name	False		False
OU3_GLN.params	segfault					name	False		False
OU3_ILE.params	segfault					name	False		False
OU3_PRO.params	segfault					name	False		False
OU3_TRP.params	segfault					name	False		False
OU3_LEU.params	segfault					name	False		False
OU3_PHE.params	segfault					name	False		False
OU3_THR.params	segfault					name	False		False
OU3_ALA.params	segfault					name	False		False
CL.params	ERROR: unrecognized atom_type_name ‘Cl1p’	anions/CL.params	CL	TYPE LIGAND	I think right now that Mini has to have at least three atoms per residue, hence the virtual atoms.	ERROR: unrecognized atom_type_name ‘Cl1p’	False		False
2S-2-amino-7-sulfanylheptanoic-acid.params	segfault					name	False		False
BPY.params		metal_binding_ncaa/BPY.params	BPY	TYPE POLYMER	ATOM FE VIRT VIRT 1.98 BOND FE NE1 PROTON_CHI 1 SAMPLES 3 60 -60 180 EXTRA 1 20 PROTON_CHI 2 SAMPLES 3 60 -60 180 EXTRA 1 20 ICOOR_INTERNAL FE -170.177941 55.215847 2.170259 NE1 CD1 CZ These lines stolen from ALA.params I believe they will override any duplicate definitions above PDB_ROTAMERS BPY.rotlib.pdb		True	N[C@H](CO)CC1CCC(C2CCCCN2)NC1	False
6-mercapto-norleucine.params	segfault					name	False		False
2.6_bisbromomethylpyridine.params	segfault					name	False		False
2.7_bisbromomethylnaphthalene.params	segfault					name	False		False
1.3.5_trisbromomethylbenzene_symm.params	segfault					name	False		False
BoronateLDopa.params	segfault					name	False		False
triazolemer_linker.params	segfault					name	False		False
1.3_bisbromomethylbenzene.params	segfault					name	False		False
1.4_bisbromomethylbenzene_symm.params	segfault					name	False		False
trimesic_acid.params		crosslinker/trimesic_acid.params	TMA	TYPE LIGAND	Trimesic acid, a non-canonical three-way crosslinking agent that can link three amine-containing amino acid residues. Params file originally created by Gauarv Bhardwaj, Ph.D. Modified and added to database by Vikram K. Mulligan, Ph.D. (vmullig@uw.edu) on 2 March 2017. Where N2 would go. Where N3 would go. Where V3 would go. Same as CONN2 Same as CONN3		True	OCC1CC(CO)CC(CO)C1	False
2.6_bisbromomethylnaphthalene.params	segfault					name	False		False
1.8_bisbromomethylnaphthalene.params	segfault					name	False		False
1.3.5_trisbromomethylbenzene.params	segfault					name	False		False
1.4_bisbromomethylbenzene.params	segfault					name	False		False
trimesic_acid_symm.params	segfault					name	False		False
1.2_bisbromomethylbenzene.params	segfault					name	False		False
PAF.params	segfault					name	False		False
QAF.params	segfault					name	False		False
QRI.params	segfault					name	False		False
KLD.params	segfault					name	False		False
KLH.params	segfault					name	False		False
QRE.params	segfault					name	False		False
KA1.params	segfault					name	False		False
TA3.params	segfault					name	False		False
UA3.params	segfault					name	False		False
MA5.params	segfault					name	False		False
LA5.params	segfault					name	False		False
OAH.params	segfault					name	False		False
QAR.params	segfault					name	False		False
PAR.params	segfault					name	False		False
QRQ.params	segfault					name	False		False
OAD.params	segfault					name	False		False
LAG.params	segfault					name	False		False
MAG.params	segfault					name	False		False
UAA.params	segfault					name	False		False
TAA.params	segfault					name	False		False
OA6.params	segfault					name	False		False
TAM.params	segfault					name	False		False
UAM.params	segfault					name	False		False
MAK.params	segfault					name	False		False
LAK.params	segfault					name	False		False
KAW.params	segfault					name	False		False
SAQ.params	segfault					name	False		False
RAQ.params	segfault					name	False		False
MAS.params	segfault					name	False		False
LAS.params	segfault					name	False		False
KL6.params	segfault					name	False		False
SAI.params	segfault					name	False		False
RAI.params	segfault					name	False		False
QA4.params	segfault					name	False		False
PA4.params	segfault					name	False		False
KAC.params	segfault					name	False		False
RAE.params	segfault					name	False		False
SAE.params	segfault					name	False		False
UAY.params	segfault					name	False		False
TAY.params	segfault					name	False		False
SAS.params	segfault					name	False		False
RAS.params	segfault					name	False		False
OA4.params	segfault					name	False		False
MAI.params	segfault					name	False		False
LAI.params	segfault					name	False		False
UAC.params	segfault					name	False		False
TAC.params	segfault					name	False		False
LAE.params	segfault					name	False		False
MAE.params	segfault					name	False		False
KAY.params	segfault					name	False		False
RAG.params	segfault					name	False		False
SAG.params	segfault					name	False		False
KAA.params	segfault					name	False		False
QR5.params	segfault					name	False		False
KAM.params	segfault					name	False		False
SAK.params	segfault					name	False		False
RAK.params	segfault					name	False		False
QA6.params	segfault					name	False		False
PA6.params	segfault					name	False		False
TAW.params	segfault					name	False		False
UAW.params	segfault					name	False		False
KL4.params	segfault					name	False		False
MAQ.params	segfault					name	False		False
LAQ.params	segfault					name	False		False
QAH.params	segfault					name	False		False
PAH.params	segfault					name	False		False
QRG.params	segfault					name	False		False
KA3.params	segfault					name	False		False
SA5.params	segfault					name	False		False
RA5.params	segfault					name	False		False
OAR.params	segfault					name	False		False
KLF.params	segfault					name	False		False
QRK.params	segfault					name	False		False
PAD.params	segfault					name	False		False
QAD.params	segfault					name	False		False
OAF.params	segfault					name	False		False
QRS.params	segfault					name	False		False
TA1.params	segfault					name	False		False
UA1.params	segfault					name	False		False
KLR.params	segfault					name	False		False
QA2.params	segfault					name	False		False
PA2.params	segfault					name	False		False
KAI.params	segfault					name	False		False
TAS.params	segfault					name	False		False
UAS.params	segfault					name	False		False
LAY.params	segfault					name	False		False
MAY.params	segfault					name	False		False
QR1.params	segfault					name	False		False
RAC.params	segfault					name	False		False
SAC.params	segfault					name	False		False
KAE.params	segfault					name	False		False
UAG.params	segfault					name	False		False
TAG.params	segfault					name	False		False
LAA.params	segfault					name	False		False
MAA.params	segfault					name	False		False
SAW.params	segfault					name	False		False
RAW.params	segfault					name	False		False
KAQ.params	segfault					name	False		False
MAM.params	segfault					name	False		False
LAM.params	segfault					name	False		False
TAK.params	segfault					name	False		False
UAK.params	segfault					name	False		False
QAT.params	segfault					name	False		False
PAT.params	segfault					name	False		False
OAN.params	segfault					name	False		False
MA3.params	segfault					name	False		False
LA3.params	segfault					name	False		False
TA5.params	segfault					name	False		False
UA5.params	segfault					name	False		False
KLV.params	segfault					name	False		False
QRW.params	segfault					name	False		False
SA1.params	segfault					name	False		False
RA1.params	segfault					name	False		False
QAL.params	segfault					name	False		False
PAL.params	segfault					name	False		False
QRC.params	segfault					name	False		False
KLN.params	segfault					name	False		False
OAV.params	segfault					name	False		False
OAL.params	segfault					name	False		False
KLT.params	segfault					name	False		False
MA1.params	segfault					name	False		False
LA1.params	segfault					name	False		False
QAV.params	segfault					name	False		False
PAV.params	segfault					name	False		False
QRY.params	segfault					name	False		False
KLL.params	segfault					name	False		False
OAT.params	segfault					name	False		False
SA3.params	segfault					name	False		False
RA3.params	segfault					name	False		False
KA5.params	segfault					name	False		False
QRA.params	segfault					name	False		False
QAN.params	segfault					name	False		False
PAN.params	segfault					name	False		False
QRM.params	segfault					name	False		False
QR3.params	segfault					name	False		False
KAG.params	segfault					name	False		False
RAA.params	segfault					name	False		False
SAA.params	segfault					name	False		False
MAW.params	segfault					name	False		False
LAW.params	segfault					name	False		False
TAQ.params	segfault					name	False		False
UAQ.params	segfault					name	False		False
KL2.params	segfault					name	False		False
RAM.params	segfault					name	False		False
KAK.params	segfault					name	False		False
TAI.params	segfault					name	False		False
UAI.params	segfault					name	False		False
OA2.params	segfault					name	False		False
KAS.params	segfault					name	False		False
RAY.params	segfault					name	False		False
SAY.params	segfault					name	False		False
LAC.params	segfault					name	False		False
MAC.params	segfault					name	False		False
UAE.params	segfault					name	False		False
TAE.params	segfault					name	False		False
PA5.params	segfault					name	False		False
QA5.params	segfault					name	False		False
RAH.params	segfault					name	False		False
KAN.params	segfault					name	False		False
LAR.params	segfault					name	False		False
MAR.params	segfault					name	False		False
UAT.params	segfault					name	False		False
TAT.params	segfault					name	False		False
QR6.params	segfault					name	False		False
KAB.params	segfault					name	False		False
SAD.params	segfault					name	False		False
RAD.params	segfault					name	False		False
MAF.params	segfault					name	False		False
LAF.params	segfault					name	False		False
KAV.params	segfault					name	False		False
UAL.params	segfault					name	False		False
TAL.params	segfault					name	False		False
PAS.params	segfault					name	False		False
QAS.params	segfault					name	False		False
OAI.params	segfault					name	False		False
UA2.params	segfault					name	False		False
KLQ.params	segfault					name	False		False
TA2.params	segfault					name	False		False
LA4.params	segfault					name	False		False
MA4.params	segfault					name	False		False
OAE.params	segfault					name	False		False
KLE.params	segfault					name	False		False
QAG.params	segfault					name	False		False
PAG.params	segfault					name	False		False
QRH.params	segfault					name	False		False
RA6.params	segfault					name	False		False
SA6.params	segfault					name	False		False
QRD.params	segfault					name	False		False
PAK.params	segfault					name	False		False
QAK.params	segfault					name	False		False
KLI.params	segfault					name	False		False
OAQ.params	segfault					name	False		False
QRR.params	segfault					name	False		False
OAG.params	segfault					name	False		False
OAK.params	segfault					name	False		False
LA6.params	segfault					name	False		False
MA6.params	segfault					name	False		False
KLS.params	segfault					name	False		False
PAQ.params	segfault					name	False		False
QAQ.params	segfault					name	False		False
KLK.params	segfault					name	False		False
OAS.params	segfault					name	False		False
KA2.params	segfault					name	False		False
RA4.params	segfault					name	False		False
SA4.params	segfault					name	False		False
PAI.params	segfault					name	False		False
QAI.params	segfault					name	False		False
QRF.params	segfault					name	False		False
QAE.params	segfault					name	False		False
PAE.params	segfault					name	False		False
KLG.params	segfault					name	False		False
QR4.params	segfault					name	False		False
SAF.params	segfault					name	False		False
RAF.params	segfault					name	False		False
UAV.params	segfault					name	False		False
KL5.params	segfault					name	False		False
TAV.params	segfault					name	False		False
KAL.params	segfault					name	False		False
LAH.params	segfault					name	False		False
MAH.params	segfault					name	False		False
UAN.params	segfault					name	False		False
TAN.params	segfault					name	False		False
OA5.params	segfault					name	False		False
RAR.params	segfault					name	False		False
SAR.params	segfault					name	False		False
KAT.params	segfault					name	False		False
MAD.params	segfault					name	False		False
LAD.params	segfault					name	False		False
QRN.params	segfault					name	False		False
QAA.params	segfault					name	False		False
PAA.params	segfault					name	False		False
KLC.params	segfault					name	False		False
OAW.params	segfault					name	False		False
PAM.params	segfault					name	False		False
QAM.params	segfault					name	False		False
KA6.params	segfault					name	False		False
LA2.params	segfault					name	False		False
MA2.params	segfault					name	False		False
UA4.params	segfault					name	False		False
KLW.params	segfault					name	False		False
TA4.params	segfault					name	False		False
QAY.params	segfault					name	False		False
PAY.params	segfault					name	False		False
QRV.params	segfault					name	False		False
OAC.params	segfault					name	False		False
TAF.params	segfault					name	False		False
UAF.params	segfault					name	False		False
OA1.params	segfault					name	False		False
LAL.params	segfault					name	False		False
MAL.params	segfault					name	False		False
RAV.params	segfault					name	False		False
SAV.params	segfault					name	False		False
UAR.params	segfault					name	False		False
KL1.params	segfault					name	False		False
TAR.params	segfault					name	False		False
LAT.params	segfault					name	False		False
MAT.params	segfault					name	False		False
KAH.params	segfault					name	False		False
RAN.params	segfault					name	False		False
SAN.params	segfault					name	False		False
PA3.params	segfault					name	False		False
QA3.params	segfault					name	False		False
KAD.params	segfault					name	False		False
KAR.params	segfault					name	False		False
RAT.params	segfault					name	False		False
SAT.params	segfault					name	False		False
OA3.params	segfault					name	False		False
UAH.params	segfault					name	False		False
TAH.params	segfault					name	False		False
LAN.params	segfault					name	False		False
MAN.params	segfault					name	False		False
TAD.params	segfault					name	False		False
UAD.params	segfault					name	False		False
KAF.params	segfault					name	False		False
QR2.params	segfault					name	False		False
RAL.params	segfault					name	False		False
PA1.params	segfault					name	False		False
QA1.params	segfault					name	False		False
LAV.params	segfault					name	False		False
MAV.params	segfault					name	False		False
KL3.params	segfault					name	False		False
RA2.params	segfault					name	False		False
SA2.params	segfault					name	False		False
KA4.params	segfault					name	False		False
KLM.params	segfault					name	False		False
OAY.params	segfault					name	False		False
KLA.params	segfault					name	False		False
QAC.params	segfault					name	False		False
PAC.params	segfault					name	False		False
QRL.params	segfault					name	False		False
KLY.params	segfault					name	False		False
OAA.params	segfault					name	False		False
QRT.params	segfault					name	False		False
PAW.params	segfault					name	False		False
QAW.params	segfault					name	False		False
UA6.params	segfault					name	False		False
TA6.params	segfault					name	False		False
OAM.params	segfault					name	False		False
MG.params	ERROR: The residue MG could not be generated. Has a suitable params file been loaded? (Note that custom params files not in the Rosetta database can be loaded with the -extra_res or -extra_res_fa command-line flags.)	metal_ions/MG.params	MG	TYPE LIGAND	I think right now that Mini has to have at least three atoms per residue, hence the virtual atoms. x y z x’ y’ z’	ERROR: The residue MG could not be generated. Has a suitable params file been loaded? (Note that custom params files not in the Rosetta database can be loaded with the -extra_res or -extra_res_fa command-line flags.)	False		False
NA.params	ERROR: The residue NA could not be generated. Has a suitable params file been loaded? (Note that custom params files not in the Rosetta database can be loaded with the -extra_res or -extra_res_fa command-line flags.)	metal_ions/NA.params	NA	TYPE LIGAND	I think right now that Mini has to have at least three atoms per residue, hence the virtual atoms.	ERROR: The residue NA could not be generated. Has a suitable params file been loaded? (Note that custom params files not in the Rosetta database can be loaded with the -extra_res or -extra_res_fa command-line flags.)	False		False
K.params	ERROR: The residue K could not be generated. Has a suitable params file been loaded? (Note that custom params files not in the Rosetta database can be loaded with the -extra_res or -extra_res_fa command-line flags.)	metal_ions/K.params	K	TYPE LIGAND	I think right now that Mini has to have at least three atoms per residue, hence the virtual atoms.	ERROR: The residue K could not be generated. Has a suitable params file been loaded? (Note that custom params files not in the Rosetta database can be loaded with the -extra_res or -extra_res_fa command-line flags.)	False		False
FE2.params		metal_ions/FE2.params	FE2	TYPE LIGAND	I think right now that Mini has to have at least three atoms per residue, hence the virtual atoms.		True	[Fe]	False
CD.params	ERROR: The residue CD could not be generated. Has a suitable params file been loaded? (Note that custom params files not in the Rosetta database can be loaded with the -extra_res or -extra_res_fa command-line flags.)	metal_ions/CD.params	CD	TYPE LIGAND	Cadmium. Added 14 June 2019 by Vikram K. Mulligan (vmulligan@flatironinstitute.org). Copied from parameters for zinc. tetrahedral geometry with 2.2 distance from center to vertex chirality is defined so that viewing from V1 to CD, V2-V3-V4 are in clockwise direction.	ERROR: The residue CD could not be generated. Has a suitable params file been loaded? (Note that custom params files not in the Rosetta database can be loaded with the -extra_res or -extra_res_fa command-line flags.)	False		False
FE.params	ERROR: The residue FE could not be generated. Has a suitable params file been loaded? (Note that custom params files not in the Rosetta database can be loaded with the -extra_res or -extra_res_fa command-line flags.)	metal_ions/FE.params	FE	TYPE LIGAND	I think right now that Mini has to have at least three atoms per residue, hence the virtual atoms.	ERROR: The residue FE could not be generated. Has a suitable params file been loaded? (Note that custom params files not in the Rosetta database can be loaded with the -extra_res or -extra_res_fa command-line flags.)	False		False
ZN.params	ERROR: The residue ZN could not be generated. Has a suitable params file been loaded? (Note that custom params files not in the Rosetta database can be loaded with the -extra_res or -extra_res_fa command-line flags.)	metal_ions/ZN.params	ZN	TYPE LIGAND	I think right now that Mini has to have at least three atoms per residue, hence the virtual atoms. tetrahedral geometry with 2.2 distance from center to vertex chirality is defined so that viewing from V1 to ZN, V2-V3-V4 are in clockwise direction.	ERROR: The residue ZN could not be generated. Has a suitable params file been loaded? (Note that custom params files not in the Rosetta database can be loaded with the -extra_res or -extra_res_fa command-line flags.)	False		False
LN.params	ERROR: unrecognized atom_type_name ‘Ln2p’	metal_ions/LN.params	LN	TYPE LIGAND	I think right now that Mini has to have at least three atoms per residue, hence the virtual atoms. x y z x’ y’ z’	ERROR: unrecognized atom_type_name ‘Ln2p’	False		False
CA.params	ERROR: The residue CA could not be generated. Has a suitable params file been loaded? (Note that custom params files not in the Rosetta database can be loaded with the -extra_res or -extra_res_fa command-line flags.)	metal_ions/CA.params	CA	TYPE LIGAND	I think right now that Mini has to have at least three atoms per residue, hence the virtual atoms. Calcium is not tetrahedral–in proteins, its coord varies from ~6-8 atoms, or 2 ions This file was changed to match properties from the centroid params file Ideal bond length is 2.4 angstroms	ERROR: The residue CA could not be generated. Has a suitable params file been loaded? (Note that custom params files not in the Rosetta database can be loaded with the -extra_res or -extra_res_fa command-line flags.)	False		False
CU.params	ERROR: The residue CU could not be generated. Has a suitable params file been loaded? (Note that custom params files not in the Rosetta database can be loaded with the -extra_res or -extra_res_fa command-line flags.)	metal_ions/CU.params	CU	TYPE LIGAND	I think right now that Mini has to have at least three atoms per residue, hence the virtual atoms. tetrahedral geometry with 2.2 distance from center to vertex chirality is defined so that viewing from V1 to CU, V2-V3-V4 are in clockwise direction.	ERROR: The residue CU could not be generated. Has a suitable params file been loaded? (Note that custom params files not in the Rosetta database can be loaded with the -extra_res or -extra_res_fa command-line flags.)	False		False
CO.params	ERROR: The residue CO could not be generated. Has a suitable params file been loaded? (Note that custom params files not in the Rosetta database can be loaded with the -extra_res or -extra_res_fa command-line flags.)	metal_ions/CO.params	CO	TYPE LIGAND	I think right now that Mini has to have at least three atoms per residue, hence the virtual atoms. tetrahedral geometry with 2.2 distance from center to vertex chirality is defined so that viewing from V1 to CO, V2-V3-V4 are in clockwise direction.	ERROR: The residue CO could not be generated. Has a suitable params file been loaded? (Note that custom params files not in the Rosetta database can be loaded with the -extra_res or -extra_res_fa command-line flags.)	False		False
MN.params	ERROR: The residue MN could not be generated. Has a suitable params file been loaded? (Note that custom params files not in the Rosetta database can be loaded with the -extra_res or -extra_res_fa command-line flags.)	metal_ions/MN.params	MN	TYPE LIGAND	I think right now that Mini has to have at least three atoms per residue, hence the virtual atoms. We don’t have a Mn type right now, but Mg should be close enough.	ERROR: The residue MN could not be generated. Has a suitable params file been loaded? (Note that custom params files not in the Rosetta database can be loaded with the -extra_res or -extra_res_fa command-line flags.)	False		False
3L2L_GALA.params	segfault					name	False		False
4L3D2L_GALA.params	segfault					name	False		False
G4ALA.params	segfault					name	False		False
4L2L_GALA.params	segfault					name	False		False
4D3D2L_GALA.params	segfault					name	False		False
G4LYS.params	segfault					name	False		False
4L3L_GALA.params	segfault					name	False		False
G2ALA.params	segfault					name	False		False
G4PHE.params	segfault					name	False		False
G4GLU.params	segfault					name	False		False
G4LEU.params	segfault					name	False		False
G3ALA.params	segfault					name	False		False
4D3L2L_GALA.params	segfault					name	False		False
4D3L_GALA.params	segfault					name	False		False
4L3L2L_GALA.params	segfault					name	False		False
3D2L_GALA.params	segfault					name	False		False
G4ASP.params	segfault					name	False		False
4D2L_GALA.params	segfault					name	False		False
GABA.params	segfault					name	False		False
G4VAL.params	segfault					name	False		False
G4TYR.params	segfault					name	False		False
BZA.params	segfault					name	False		False
BZO.params	segfault					name	False		False
ACE.params	segfault					name	False		False
NME.params	segfault					name	False		False
GPN.params		pna/GPN.params	GPN	TYPE POLYMER	PROTEIN for termini; PEPTOID because of where the SC comes off… not sure. Old: ICOOR_INTERNAL UPPER 1.300000 60.487741 1.342337 C CD2 NG ICOOR_INTERNAL O -126.716072 60.551385 1.205654 C CD2 NG Below: from ALA ICOOR_INTERNAL UPPER 149.999985 63.800007 1.328685 C CA N ICOOR_INTERNAL O -180.000000 59.200005 1.231015 C CA UPPER		True	NCCN(CCO)C(O)CN1CNC2C(O)NC(N)NC21	False
APN.params		pna/APN.params	APN	TYPE POLYMER	PROTEIN for termini; PEPTOID because of where the SC comes off… not sure. ICOOR_INTERNAL UPPER 1.300000 60.487741 1.342337 C CD2 NG ICOOR_INTERNAL O -126.716072 60.551385 1.205654 C CD2 NG ICOOR_INTERNAL 1HA -120.796669 71.362736 1.082254 CA CB NG ICOOR_INTERNAL 2HA 117.569665 71.501926 1.081810 CA CB 1HA		True	NCCN(CCO)C(O)CN1CNC2C(N)NCNC21	False
TPN.params		pna/TPN.params	TPN	TYPE POLYMER	PROTEIN for termini; PEPTOID because of where the SC comes off… not sure. ICOOR_INTERNAL UPPER 1.300000 60.487741 1.342337 C CD2 NG ICOOR_INTERNAL O -126.716072 60.551385 1.205654 C CD2 NG		True	CC1CN(C[C@@H](O)N(CCN)CCO)C(O)NC1O	False
UPN.params		pna/UPN.params	UPN	TYPE POLYMER	PROTEIN for termini; PEPTOID because of where the SC comes off… not sure. ICOOR_INTERNAL UPPER 1.300000 60.487741 1.342337 C CD2 NG ICOOR_INTERNAL O -126.716072 60.551385 1.205654 C CD2 NG		True	NCCN(CCO)[C@H](O)CN1CCC(O)NC1O	False
CPN.params		pna/CPN.params	CPN	TYPE POLYMER	PROTEIN for termini; PEPTOID because of where the SC comes off… not sure. ICOOR_INTERNAL UPPER 1.300000 60.487741 1.342337 C CD2 NG ICOOR_INTERNAL O -126.716072 60.551385 1.205654 C CD2 NG		True	NCCN(CCO)C(O)CN1CCC(N)NC1O	False
INV_VRT.params	segfault					name	False		False
VRT1.params	segfault					name	False		False
VRT.params	segfault					name	False		False
GB_AA_PLACEHOLDER.params	segfault					name	False		False
SUCK.params	segfault					name	False		False
VRTBB.params	segfault					name	False		False
sphingosine.params	segfault					name	False		False
nBuOH.params	segfault					name	False		False
choline.params	segfault					name	False		False
linoleate.params	segfault					name	False		False
palmitate.params	segfault					name	False		False
oleate.params	segfault					name	False		False
ONonOMe.params	segfault					name	False		False
glycerol-3-phosphate.params	segfault					name	False		False
CRO.params	segfault					name	False		False
C.params	segfault					name	False		False
2-iodophenol.params	segfault					name	False		False
LYX.params	segfault					name	False		False
DGLX.params	segfault					name	False		False
GLX.params	segfault					name	False		False
DLYX.params	segfault					name	False		False
VLS.params		sidechain_conjugation/VLS.params	VLS	TYPE POLYMER	CHI 5 CD CE NZ CT CHI 6 CE NZ CT CI2 CHI 7 NZ CT CI2 CK		True	CCC(O)NCCCC[C@H](N)CO	False
DASX.params	segfault					name	False		False
ASX.params	segfault					name	False		False
ALT.params		sidechain_conjugation/ALT.params	ALT	TYPE POLYMER	azidolysine triazole, polymer part TYPES SC_BRANCH_POINT CHI 5 CD CE NZ NT ICOOR_INTERNAL CONN4 -176.937537 75.989168 1.357280 NI1 NZ CE		True	NNNCCCC[C@H](N)CO	False
PET.params	segfault					name	False		False
VDP.params		sidechain_conjugation/VDP.params	VDP	TYPE POLYMER	ICOOR_INTERNAL CD -106.487167 53.797996 1.367111 NG CB CA ICOOR_INTERNAL 1HG 34.430666 64.693346 1.000341 NG CB CD ROTAMER_AA MET BACKBONE_AA MET		True	CC[C@H](O)NC[C@H](N)CO	False
VHA.params		sidechain_conjugation/VHA.params	VHA	TYPE POLYMER	CHI 3 CB CG ND CE		True	CCC(O)NCC[C@H](N)CO	False
CYX.params		sidechain_conjugation/CYX.params	CYX	TYPE POLYMER	rosetta residue topology file icoor for connect-bond is from 1FXT, which contains a CYX - Glycine bond Updated 11 April 2014 by Vikram K. Mulligan, Baker laboratory. residue type APL O to CB distance – max O-CB observed in ubiquitin Same as CONN3		True	NC(CO)CS	False
VOR.params		sidechain_conjugation/VOR.params	VOR	TYPE POLYMER	CHI 5 CD NE CZ CT2 CHI 6 NE CZ CT2 CI		True	CCC(O)NCCC[C@H](N)CO	False
VSR.params		sidechain_conjugation/VSR.params	VSR	TYPE POLYMER	CHI 3 CB OG CD CE2		True	CCC(O)OC[C@H](N)CO	False
OSi.params		mineral_surface/OSi.params	OSi	TYPE LIGAND	I think right now that Mini has to have at least three atoms per residue, hence the virtual atoms. Correct later		True	O	False
CAL.params	ERROR: add_bond: atom Ca2p and/or V don’t exist!	mineral_surface/CAL.params	CAL	TYPE LIGAND	created by liza lee (Graylab@JHU) For hydroxyapatite surface parameters are from Kosta Makrodimitris’s Ca2p.params		True		False
OHH.params		mineral_surface/OHH.params	OHH	TYPE LIGAND	created by liza lee (Graylab@JHU) For oxygen of hydroxyl in hydroxyapatite surface		True	O	False
CO3.params		mineral_surface/CO3.params	CO3	TYPE LIGAND			True	OC(O)O	False
Si.params	ERROR: The residue Si could not be generated. Has a suitable params file been loaded? (Note that custom params files not in the Rosetta database can be loaded with the -extra_res or -extra_res_fa command-line flags.)	mineral_surface/Si.params	Si	TYPE LIGAND	I think right now that Mini has to have at least three atoms per residue, hence the virtual atoms. Correct later	ERROR: The residue Si could not be generated. Has a suitable params file been loaded? (Note that custom params files not in the Rosetta database can be loaded with the -extra_res or -extra_res_fa command-line flags.)	False		False
OC3.params	ERROR: add_bond: atom OC3 and/or V don’t exist!	mineral_surface/OC3.params	OC3	TYPE LIGAND	I think right now that Mini has to have at least three atoms per residue, hence the virtual atoms.		True		False
HHA.params		mineral_surface/HHA.params	HHA	TYPE LIGAND	created by liza lee (Graylab@JHU) For hydrogen of hydroxyl ion in hydroxyapatite surface distance beyond which residue i and j would not be neighbors		True	[HH]	False
Oice.params	segfault					name	False		False
HYD.params		mineral_surface/HYD.params	HYD	TYPE LIGAND	created by liza lee (Graylab@JHU) For hydroxyl ion in monoclinic hydroxyapatite surface		True	O	False
OPH.params		mineral_surface/OPH.params	OPH	TYPE LIGAND	created by liza lee (Graylab@JHU) For oxygen of phosphate in hydroxyapatite		True	O	False
PHA.params		mineral_surface/PHA.params	PHA	TYPE LIGAND	created by liza lee (Graylab@JHU) For phosphorous of phosphate in monoclinic hydroxypatite surface		True	P	False
Hice.params	segfault					name	False		False
PHO.params		mineral_surface/PHO.params	PHO	TYPE LIGAND	created by liza lee (Graylab@JHU) For phosphate ion in monoclinic hydroxyapatite surface		True	O[PH](O)(O)O	False
104.params		peptoids/104.params	104	TYPE POLYMER	Amine submonomer: 2-chloro benzyl amine		True	OCCNC[C@H]1CCCCC1Cl	False
004.params		peptoids/004.params	004	TYPE POLYMER	Amine submonomer: 2-methyl 3-hydroxy aniline		True	CC1C(O)CCCC1NCCO	False
016.params		peptoids/016.params	016	TYPE POLYMER	Amine submonomer: not loaded		True	COC1CC(NCCO)CCN1	False
116.params		peptoids/116.params	116	TYPE POLYMER	Amine submonomer: 4-fluoro benzyl amine		True	OCCNCC1CCC(F)CC1F	False
008.params		peptoids/008.params	008	TYPE POLYMER	Amine submonomer: ? won’t load’		True	OCCNC1CCCC2OCCOC12	False
108.params		peptoids/108.params	108	TYPE POLYMER	Amine submonomer: not loaded		True	COC1CCC(CNCCO)CC1OC	False
020.params		peptoids/020.params	020	TYPE POLYMER	Amine submonomer: 1-amino napthalene		True	OCCNC1CCCC2CCCCC21	False
120.params		peptoids/120.params	120	TYPE POLYMER	Amine submonomer: 2, 4-dichloro benzyl amine		True	OCCNCC1CCC(Cl)CC1Cl	False
132.params		peptoids/132.params	132	TYPE POLYMER	Amine submonomer: 1-hydroxy-cyclohexyl methyl amine		True	OCCNCC1(O)CCCCC1	False
403.params	ERROR: Can’t add atom named ` CA ` to ResidueType as it already has one with that name.	peptoids/403.params	403	TYPE POLYMER	Amine submonomer: 2,4 dichloro homobenzyl amine	ERROR: Can’t add atom named ` CA ` to ResidueType as it already has one with that name.	False		False
503.params		peptoids/503.params	503	TYPE POLYMER	Amine submonomer: not loaded		True	OCCNCC[C@@H]1CN[C@@H]2CCCCC12	False
411.params		peptoids/411.params	411	TYPE POLYMER	Amine submonomer: 2,3 dihydro 1H-inden-2-amine		True	OCCNC1CC2CCCCC2C1	False
315.params		peptoids/315.params	315	TYPE POLYMER	Amine submonomer: diaminomethane		True	[NH3+]CNCCO	False
307.params		peptoids/307.params	307	TYPE POLYMER	Amine submonomer: 3-hydroxy propylamine		True	OCCCNCCO	False
207.params		peptoids/207.params	207	TYPE POLYMER	Amine submonomer: not loaded - identical to 204		True	CCCCNCCO	False
413.params	In chi #3, the base of the fourth atom ( CD1) is CE1, rather than the third atom of the chi ( NG )	peptoids/413.params	413	TYPE POLYMER	Amine submonomer: 2-morpholine ethylamine	In chi #3, the base of the fourth atom ( CD1) is CE1, rather than the third atom of the chi ( NG )	False		False
401.params		peptoids/401.params	401	TYPE POLYMER	Amine submonomer: homobenzyl amine		True	OCCNCCC1CCCCC1	False
501.params		peptoids/501.params	501	TYPE POLYMER	Amine submonomer: not loaded		True	OCCNCC1CCCO1	False
333.params		peptoids/333.params	333	TYPE POLYMER	A peptoid with an ornithine-like sidechain. Params file added by Vikram K. Mulligan, Flatiron Institute (vmulligan@flatironinstitute.org) on 26 Nov. 2018. Geometry generated in Avogadro, and optimized first with MM (MMFF94s force field) and second with QM methods using GAMESS (STO-6G approximation). Partial charges were recomputed with the 6-311G approximation. there was no change in the values. Note: I’ll use the convention of 33x = lysine-like sidechain with x methylene groups.		True	[NH3+]CCCNCCO	False
305.params		peptoids/305.params	305	TYPE POLYMER	Amine submonomer: 2-methoxy ethylamine		True	COCCNCCO	False
205.params		peptoids/205.params	205	TYPE POLYMER	Amine submonomer: 3-methyl butyl 1-amine		True	CC(C)CCNCCO	False
209.params		peptoids/209.params	209	TYPE POLYMER	Amine submonomer: cyclopentyl methylamine		True	CCC(CC)CNCCO	False
309.params	ERROR: Can’t add atom named ` CA ` to ResidueType as it already has one with that name.	peptoids/309.params	309	TYPE POLYMER	nonsense	ERROR: Can’t add atom named ` CA ` to ResidueType as it already has one with that name.	False		False
317.params		peptoids/317.params	317	TYPE POLYMER	Amine submonomer: diaminopropane		True	[NH3+]CCCNCCO	False
014.params		peptoids/014.params	014	TYPE POLYMER	Amine submonomer: not loaded		True	OCCN[C@@]1(N(O)O)CCCCC1O	False
114.params		peptoids/114.params	114	TYPE POLYMER	Amine submonomer: 2,5-difluoro benzyl amine		True	OCCNCC1C(F)CCCC1F	False
118.params		peptoids/118.params	118	TYPE POLYMER	Amine submonomer: 2,3 fluorobenzyl amine		True	OCCNCC1CCCC(F)C1F	False
018.params	In chi #1, the base of the fourth atom ( CB1) is CG2, rather than the third atom of the chi ( CA1)	peptoids/018.params	018	TYPE POLYMER	Amine submonomer: 2-hydroxyl aniline	In chi #1, the base of the fourth atom ( CB1) is CG2, rather than the third atom of the chi ( CA1)	False		False
106.params		peptoids/106.params	106	TYPE POLYMER	Amine submonomer: not loaded		True	OCCNCC1CCCC(Cl)C1	False
006.params		peptoids/006.params	006	TYPE POLYMER	Amine submonomer: 3, 4-dimethyl-5 hydroxy aniline		True	CC1CC(NCCO)CC(O)C1C	False
702.params	In chi #2, the base of the fourth atom ( N ) is CA , rather than the third atom of the chi ( CA1)	peptoids/702.params	702	TYPE POLYMER	Amine submonomer: half of a click	In chi #2, the base of the fourth atom ( N ) is CA , rather than the third atom of the chi ( CA1)	False		False
130.params		peptoids/130.params	130	TYPE POLYMER	Amine submonomer: diphenyl methyl amine		True	OCCNC(C1CCCCC1)C1CCCCC1	False
122.params		peptoids/122.params	122	TYPE POLYMER	Amine submonomer: not loaded		True	OCCNCC1CCCCN1	False
313.params		peptoids/313.params	313	TYPE POLYMER	Amine submonomer: carboxy methylamine (asp-ish) This sidechain matches that of aspartate (ASP).		True	OCCNCC(O)O	False
405.params		peptoids/405.params	405	TYPE POLYMER	Amine submonomer: not loaded		True	OCCNCCC1CCCC(O)C1	False
505.params		peptoids/505.params	505	TYPE POLYMER	Amine submonomer: not loaded		True	OCCNCC[C@@H]1CN[C@@H]2CC(Cl)CCC12	False
509.params		peptoids/509.params	509	TYPE POLYMER	Amine submonomer: not loaded		True	OCCNCCC1NC2CCCCC2N1	False
409.params		peptoids/409.params	409	TYPE POLYMER	Amine submonomer: not loaded		True	OCCNCCC1CCCC(N(O)O)N1	False
126.params		peptoids/126.params	126	TYPE POLYMER	Amine submonomer: not loaded		True	CC1CNC(CNCCO)CN1	False
102.params		peptoids/102.params	102	TYPE POLYMER	Amine submonomer: 3-chloro benzyl amine		True	OCCNCC1CCCC(Cl)C1	False
002.params		peptoids/002.params	002	TYPE POLYMER	Amine submonomer: not loaded		True	OCCNC1CCCC(OC2CCCCC2)C1	False
010.params		peptoids/010.params	010	TYPE POLYMER	Amine submonomer: not loaded		True	OCCNC1CCCC(O)C1O	False
110.params		peptoids/110.params	110	TYPE POLYMER	Amine submonomer: not loaded		True	COC1CC(CNCCO)CC(OC)C1	False
128.params		peptoids/128.params	128	TYPE POLYMER	Amine submonomer: 2-methyl napthalene - amine		True	OCCNCC1CCC2CCCCC2C1	False
704.params		peptoids/704.params	704	TYPE POLYMER	Amine submonomer: half of a click		True	NNCCCNCCO	False
124.params		peptoids/124.params	124	TYPE POLYMER	Amine submonomer: not loaded		True	OCCNCC1CCCNC1	False
012.params		peptoids/012.params	012	TYPE POLYMER	Amine submonomer: not loaded		True	OCCNC1CCCC(O)C1N(O)O	False
112.params		peptoids/112.params	112	TYPE POLYMER	Amine submonomer: not loaded		True	OCCNCC1CCC2OCOC2C1	False
303.params		peptoids/303.params	303	TYPE POLYMER	Amine submonomer: ethanolamine		True	OCCNCCO	False
203.params		peptoids/203.params	203	TYPE POLYMER	Amine submonomer: propyl amine		True	CCCNCCO	False
211.params		peptoids/211.params	211	TYPE POLYMER	Amine submonomer: isopropyl amine This sidechain is that of valine (VAL).		True	CC(C)NCCO	False
407.params		peptoids/407.params	407	TYPE POLYMER	Amine submonomer: not loaded		True	COC1CCCC(CCNCCO)C1	False
507.params		peptoids/507.params	507	TYPE POLYMER	Amine submonomer: not loaded		True	OCCNCCC1NCCN1	False
314.params		peptoids/314.params	314	TYPE POLYMER	Amine submonomer: carboxy ethylamine (glu-ish) This sidechain matches that of glutamate (GLU).		True	OCCNCCC(O)O	False
318.params		peptoids/318.params	318	TYPE POLYMER	Amine submonomer: diaminobutane		True	[NH3+]CCCCNCCO	False
206.params	segfault					name	False		False
306.params		peptoids/306.params	306	TYPE POLYMER	Amine submonomer: 3-methoxy propylamine		True	COCCCNCCO	False
502.params		peptoids/502.params	502	TYPE POLYMER	Amine submonomer: not loaded		True	OCCNCCC1CCCO1	False
402.params		peptoids/402.params	402	TYPE POLYMER	Amine submonomer: not loaded		True	OCCNCCC1CCCC(Cl)C1	False
410.params		peptoids/410.params	410	TYPE POLYMER	Amine submonomer: 2-fluoro homobenzyl amine		True	OCCNCCC1CCCC[C@@H]1F	False
121.params		peptoids/121.params	121	TYPE POLYMER	Amine submonomer: not loaded		True	OCCNCC1CCCCC1Cl	False
021.params	In chi #1, the base of the fourth atom ( CB1) is CG1, rather than the third atom of the chi ( CA1)	peptoids/021.params	021	TYPE POLYMER	Amine submonomer: 2-methyl 4-hydroxy aniline	In chi #1, the base of the fourth atom ( CB1) is CG1, rather than the third atom of the chi ( CA1)	False		False
701.params		peptoids/701.params	701	TYPE POLYMER	Amine submonomer: half of a click		True	CC(N)CNCCO	False
601.params		peptoids/601.params	601	TYPE POLYMER	Amine submonomer: beta-methyl benzyl amine/ S phenylethyl-1-amine (Nspe ) This resembles a phenylalanine side-chain (coming off of the nitrogen, of course), but with an extra methyl group on what would be the methylene (CB) atom. This makes this peptoid chiral (only in the side-chain).		True	C[C@H](NCCO)C1CCCCC1	False
005.params		peptoids/005.params	005	TYPE POLYMER	Amine submonomer: 3-phenyl aniline		True	OCCNC1CCCC(C2CCCCC2)C1	False
105.params		peptoids/105.params	105	TYPE POLYMER	Amine submonomer: not loaded		True	OCCNC[C@@H]1CCCCC1N(O)O	False
109.params		peptoids/109.params	109	TYPE POLYMER	Amine submonomer: not loaded		True	OCCNCC1CCC(N(O)O)CC1	False
009.params		peptoids/009.params	009	TYPE POLYMER	Amine submonomer: 2, 3 dihydro 1H inden-4-amine		True	OCCNC1CCCC2CCCC21	False
117.params		peptoids/117.params	117	TYPE POLYMER	Amine submonomer: 3-fluorobenzyl amine		True	OCCNCC1CCCC(F)C1	False
017.params	In chi #1, the base of the fourth atom ( CB1) is CG1, rather than the third atom of the chi ( CA1)	peptoids/017.params	017	TYPE POLYMER	Amine submonomer: 4-hydroxyl aniline (i.e. tyr)	In chi #1, the base of the fourth atom ( CB1) is CG1, rather than the third atom of the chi ( CA1)	False		False
131.params		peptoids/131.params	131	TYPE POLYMER	Amine submonomer: not loaded		True	OCCNCC1CCC2CCCC(O)C2N1	False
703.params		peptoids/703.params	703	TYPE POLYMER	Amine submonomer: half of a click		True	NNCCNCCO	False
123.params		peptoids/123.params	123	TYPE POLYMER	Amine submonomer: not loaded		True	OCCNCC1CCCC(Cl)C1	False
115.params		peptoids/115.params	115	TYPE POLYMER	Amine submonomer: 2-fluoro benzyl amine		True	OCCNCC1CCCCC1F	False
015.params		peptoids/015.params	015	TYPE POLYMER	Amine submonomer: not loaded		True	COC1CCCC(NCCO)C1	False
007.params		peptoids/007.params	007	TYPE POLYMER	Amine submonomer: 2,3 dimethyl aniline		True	CC1CCCC(NCCO)C1C	False
107.params		peptoids/107.params	107	TYPE POLYMER	Amine submonomer: not loaded		True	OCCNCC1CCCC(N(O)O)C1	False
019.params	In chi #1, the base of the fourth atom ( CB1) is CG1, rather than the third atom of the chi ( CA1)	peptoids/019.params	019	TYPE POLYMER	Amine submonomer: 2,3-dimethyl 4-hydroxy aniline	In chi #1, the base of the fourth atom ( CB1) is CG1, rather than the third atom of the chi ( CA1)	False		False
119.params		peptoids/119.params	119	TYPE POLYMER	Amine submonomer: not used (symmetry to 117)		True	OCCNCC1CCCC(F)C1	False
204.params		peptoids/204.params	204	TYPE POLYMER	Amine submonomer: butyl amine		True	CCCCNCCO	False
304.params		peptoids/304.params	304	TYPE POLYMER	Amine submonomer: not loaded 2-(dimethylamino) propylamine		True	CN(C)CCCNCCO	False
316.params		peptoids/316.params	316	TYPE POLYMER	Amine submonomer: ethylenediamine		True	[NH3+]CCNCCO	False
308.params	ERROR: Can’t add atom named ` CA ` to ResidueType as it already has one with that name.	peptoids/308.params	308	TYPE POLYMER	nonsense	ERROR: Can’t add atom named ` CA ` to ResidueType as it already has one with that name.	False		False
208.params		peptoids/208.params	208	TYPE POLYMER	Amine submonomer: isobutyl amine This sidechain is like that of leucine (LEU).		True	CC(C)CNCCO	False
320.params		peptoids/320.params	320	TYPE POLYMER	Amine submonomer: 3-(dimethylamino)-2,2-dimethyl propyl amine		True	C[NH+](C)CC(C)(C)CNCCO	False
412.params		peptoids/412.params	412	TYPE POLYMER	Amine submonomer: 3-fluoro homobenzyl amine		True	OCCNCCC1CCCC(F)C1	False
332.params		peptoids/332.params	332	TYPE POLYMER	A peptoid with a side-chain like DAB (2,4-diaminobutyric acid). Params file added by Vikram K. Mulligan, Flatiron Institute (vmulligan@flatironinstitute.org) on 26 November 2018. The geometry was created in Avogadro, and optimized first with molecular mechanics (MMFF94s force field), and then with QM methods (STO-6G approximation) using GAMESS. Note: I’ll use the convention of 33x = lysine-like sidechain with x methylene groups.		True	[NH3+]CCNCCO	False
003.params		peptoids/003.params	003	TYPE POLYMER	Amine submonomer: 3-tertbutyl aniline		True	CC(C)(C)C1CCCC(NCCO)C1	False
103.params		peptoids/103.params	103	TYPE POLYMER	Amine submonomer: 2-methyl benzyl amine		True	CC1CCCCC1CNCCO	False
631.params		peptoids/631.params	631	TYPE POLYMER	A peptoid with a side-chain like D-threonine or L-allo-threonine. This is N-((S)-1-hydroxyethyl)glycine. Params file added by Vikram K. Mulligan, Flatiron Institute (vmulligan@flatironinstitute.org) on 8 Nov. 2018.		True	C[C@H](O)NCCO	False
111.params		peptoids/111.params	111	TYPE POLYMER	Amine submonomer: 3-hydroxy benzyl amine		True	OCCNCC1CCCC(O)C1	False
011.params	ERROR: Can’t add atom named ` CA ` to ResidueType as it already has one with that name.	peptoids/011.params	011	TYPE POLYMER	Amine submonomer: not loaded	ERROR: Can’t add atom named ` CA ` to ResidueType as it already has one with that name.	False		False
623.params		peptoids/623.params	623	TYPE POLYMER	Amine submonomer: S cyclohexylethyl-1-amine (Nsce)		True	C[C@@H](NCCO)C1CCCCC1	False
127.params		peptoids/127.params	127	TYPE POLYMER	Amine submonomer: 1-methyl napthalene - amine		True	OCCNCC1CCCC2CCCCC21	False
504.params		peptoids/504.params	504	TYPE POLYMER	Amine submonomer: not loaded		True	CC1CCC(CNCCO)O1	False
404.params		peptoids/404.params	404	TYPE POLYMER	Amine submonomer: not loaded		True	COC1CCC(CCNCCO)CC1OC	False
408.params		peptoids/408.params	408	TYPE POLYMER	Amine submonomer: not loaded		True	OCCNCCC1CCCCN1	False
508.params		peptoids/508.params	508	TYPE POLYMER	Amine submonomer: not loaded		True	OCCNCCCN1CCNC1	False
506.params	ERROR: Can’t add atom named ` CA ` to ResidueType as it already has one with that name.	peptoids/506.params	506	TYPE POLYMER	Amine submonomer: not loaded	ERROR: Can’t add atom named ` CA ` to ResidueType as it already has one with that name.	False		False
406.params		peptoids/406.params	406	TYPE POLYMER	Amine submonomer: 2,4 dichloro homobenzyl amine		True	OCCNCCC1CCC(Cl)CC1Cl	False
202.params		peptoids/202.params	202	TYPE POLYMER	Amine submonomer: ethyl amine		True	CCNCCO	False
302.params		peptoids/302.params	302	TYPE POLYMER	Amine submonomer: not loaded 2-(dimethylamino) ethylamine		True	CN(C)CCNCCO	False
210.params		peptoids/210.params	210	TYPE POLYMER	Amine submonomer: cyclopropyl methyl amine		True	OCCNCC1CC1	False
621.params		peptoids/621.params	621	TYPE POLYMER	Amine submonomer: beta-methyl napthyl amine/ S 1-napthylethylamine (Nsna)		True	C[C@H](NCCO)C1CCCC2CCCCC21	False
113.params		peptoids/113.params	113	TYPE POLYMER	Amine submonomer: not loaded		True	COC1CCCC(CNCCO)C1	False
013.params		peptoids/013.params	013	TYPE POLYMER	Amine submonomer: 3-hydroxy aniline		True	OCCNC1CCCC(O)C1	False
633.params		peptoids/633.params	633	TYPE POLYMER	A peptoid with a side-chain like D-threonine or L-allo-threonine, with an extra hydroxyl on the terminal methyl group. This is N-((S)-1,2-dihydroxyethyl)glycine. Params file added by Vikram K. Mulligan, Flatiron Institute (vmulligan@flatironinstitute.org) on 9 Nov. 2018.		True	OCCN[C@@H](O)CO	False
001.params		peptoids/001.params	001	TYPE POLYMER	Amine submonomer: aniline		True	OCCNC1CCCCC1	False
101.params		peptoids/101.params	101	TYPE POLYMER	Amine submonomer: benzyl amine This is equivalent to a phenylalanine (PHE) side-chain, albeit on the amide nitrogen instead of on the alpha carbon.		True	OCCNCC1CCCCC1	False
129.params		peptoids/129.params	129	TYPE POLYMER	Amine submonomer: 4-amino N-benzyl piperidine		True	OCCNC1CCN(CC2CCCCC2)CC1	False
125.params		peptoids/125.params	125	TYPE POLYMER	Amine submonomer: not loaded		True	OCCNCC1CCNCC1	False
TYR.params		l-caa/TYR.params	TYR	TYPE POLYMER	rosetta residue topology file residue type In rare cases, a tyrosine coordinates a metal with its side-chain oxygen. APL CB to sidechain heavyatom distance – max observed at residue 74 in ubiquitin ACT_COORD_ATOMS CG CZ END hack to make it run for now…		True	N[C@H](C=O)Cc1ccc(O)cc1	False
CYS.params		l-caa/CYS.params	CYS	TYPE POLYMER	rosetta residue topology file residue type APL O to CB distance – max O-CB observed in ubiquitin		True	N[C@H](C=O)CS	False
ASN.params		l-caa/ASN.params	ASN	TYPE POLYMER	rosetta residue topology file residue type APL O to CB distance; max observed in ubiquitin		True	NC(=O)C[C@H](N)C=O	False
MET.params	ATOM_ALIAS SD SE	l-caa/MET.params	MET	TYPE POLYMER	rosetta residue topology file residue type For MSE recognition Note that, for convenience, we classify methionine as an “honorary” aliphatic: There are rare cases in which the delta sulfur coordinates a metal. APL CB to sidechain heavyatom distance; swept all chi combos at 5 degree intervals		True		False
ILE.params		l-caa/ILE.params	ILE	TYPE POLYMER	rosetta residue topology file residue type APL O to CB distance; max observed in ubiquitin		True	CC[C@H](C)[C@H](N)C=O	False
GLN.params	ATOM_ALIAS 1HB HB2	l-caa/GLN.params	GLN	TYPE POLYMER	rosetta residue topology file residue type APL CB to sidechain heavyatom distance – max observed at residue 74 in ubiquitin		True		False
VAL.params		l-caa/VAL.params	VAL	TYPE POLYMER	rosetta residue topology file residue type Max distance from C-Beta to the members of the backbone; 3.4473 in all canonical AAs.		True	CC(C)[C@H](N)C=O	False
TRP.params		l-caa/TRP.params	TRP	TYPE POLYMER	rosetta residue topology file residue type APL CB to sidechain heavyatom distance; swept all chi combos at 5 degree intervals		True	N[C@H](C=O)Cc1c[nH]c2ccccc12	False
ASP.params	segfault					name	False		False
PRO.params	ATOM_ALIAS 1HB HB2	l-caa/PRO.params	PRO	TYPE POLYMER	rosetta residue topology file residue type APL Declare that the NV atom should shadow the N atom to the cart-bonded term. APL O to CB distance; max observed in ubiquitin		True		False
SER.params		l-caa/SER.params	SER	TYPE POLYMER	rosetta residue topology file residue type APL O to CB distance; max observed in ubiquitin		True	N[C@H](C=O)CO	False
LEU.params		l-caa/LEU.params	LEU	TYPE POLYMER	rosetta residue topology file residue type APL O to CB distance; max observed in ubiquitin		True	CC(C)C[C@H](N)C=O	False
GLU.params	segfault					name	False		False
GLY.params		l-caa/GLY.params	GLY	TYPE POLYMER	rosetta residue topology file residue type APL CA to O distance – not yet measured; default to max CB to O distance		True	NCC=O	False
PHE.params		l-caa/PHE.params	PHE	TYPE POLYMER	rosetta residue topology file residue type APL CB to side chain heavyatom distance – max as observed on residue 74 of ubiquitin		True	N[C@H](C=O)Cc1ccccc1	False
LYS.params	ATOM_ALIAS 1HB HB2	l-caa/LYS.params	LYS	TYPE POLYMER	rosetta residue topology file residue type APL CB to side chain heavyatom distance – max observed in residue 74 of ubiquitin		True		False
THR.params		l-caa/THR.params	THR	TYPE POLYMER	rosetta residue topology file residue type APL O to CB distance; max observed in ubiquitin		True	C[C@@H](O)[C@H](N)C=O	False
ARG.params	segfault					name	False		False
ALA.params	ATOM_ALIAS 1HB HB1	l-caa/ALA.params	ALA	TYPE POLYMER	rosetta residue topology file residue type APL O to CB DISTANCE – MAX O-CB OBSERVED IN UBQ		True		False
HIS_D.params	segfault					name	False		False
HIS.params		l-caa/HIS.params	HIS	TYPE POLYMER	rosetta residue topology file residue type APL CB to sidechain heavy atom disance – max observed on residue 74 of ubiquitin		True	N[C@H](C=O)Cc1c[nH]cn1	False
CYV.params		l-caa/CYV.params	CYS	TYPE POLYMER	rosetta residue topology file CYS withVCB andVSG defined as virtual residue type APL O toVCB distance – max O-CB observed in ubiquitin		True	NCC=O	False
CYZ.params		l-caa/CYZ.params	CYS	TYPE POLYMER	rosetta residue topology file CYS with HG defined as virtual residue type APL O to CB distance – max O-CB observed in ubiquitin		True	N[C@H](C=O)CS	False
isoprene.params	segfault					name	False		False
AIB.params		achiral_ncaa/AIB.params	AIB	TYPE POLYMER	Params file defining topology for 2-aminoisobutyric acid (AIB), an achiral amino acid that strongly favours alpha-helices. Params file by Tim Craven; modified by Vikram K. Mulligan. Added 13 February 2017.		True	CC(C)(N)CO	False
UDP.params	segfault					name	False		False
flavin_oxidized.params	segfault					name	False		False
flavin_reduced.params	segfault					name	False		False
SAM.params	segfault					name	False		False
SAH.params	segfault					name	False		False
ATP.params	segfault					name	False		False
flavin_mononucleotide.params	segfault					name	False		False
DHA.params	segfault					name	False		False
D-Eul.params	segfault					name	False		False
L-Eul.params	segfault					name	False		False
to5-beta-Kdop.params	segfault					name	False		False
to8-alpha-Kdop.params	segfault					name	False		False
to4-beta-Kdop.params	segfault					name	False		False
to7-beta-Kdop.params	segfault					name	False		False
to8-beta-Kdop.params	segfault					name	False		False
to7-alpha-Kdop.params	segfault					name	False		False
to4-alpha-Kdop.params	segfault					name	False		False
to5-alpha-Kdop.params	segfault					name	False		False
to3-beta-L-Psip.params	segfault					name	False		False
to1-alpha-D-Psip.params	segfault					name	False		False
to3-alpha-D-Psip.params	segfault					name	False		False
to5-alpha-D-Psip.params	segfault					name	False		False
to4-alpha-D-Psip.params	segfault					name	False		False
to4-beta-D-Psip.params	segfault					name	False		False
to5-beta-L-Psip.params	segfault					name	False		False
to1-beta-D-Psip.params	segfault					name	False		False
to4-alpha-L-Psip.params	segfault					name	False		False
to5-alpha-L-Psip.params	segfault					name	False		False
to4-beta-L-Psip.params	segfault					name	False		False
to1-alpha-L-Psip.params	segfault					name	False		False
to3-beta-D-Psip.params	segfault					name	False		False
to3-alpha-L-Psip.params	segfault					name	False		False
to1-beta-L-Psip.params	segfault					name	False		False
to5-beta-D-Psip.params	segfault					name	False		False
to5-beta-D-Sorp.params	segfault					name	False		False
to1-beta-L-Sorp.params	segfault					name	False		False
to5-alpha-L-Sorp.params	segfault					name	False		False
to4-alpha-L-Sorp.params	segfault					name	False		False
to4-beta-L-Sorp.params	segfault					name	False		False
to3-beta-D-Sorp.params	segfault					name	False		False
to1-alpha-L-Sorp.params	segfault					name	False		False
to3-alpha-L-Sorp.params	segfault					name	False		False
to1-beta-D-Sorp.params	segfault					name	False		False
to5-beta-L-Sorp.params	segfault					name	False		False
to1-alpha-D-Sorp.params	segfault					name	False		False
to3-beta-L-Sorp.params	segfault					name	False		False
to3-alpha-D-Sorp.params	segfault					name	False		False
to4-alpha-D-Sorp.params	segfault					name	False		False
to5-alpha-D-Sorp.params	segfault					name	False		False
to4-beta-D-Sorp.params	segfault					name	False		False
to1-beta-L-Frup.params	segfault					name	False		False
to5-beta-D-Frup.params	segfault					name	False		False
to4-beta-L-Frup.params	segfault					name	False		False
to4-alpha-L-Frup.params	segfault					name	False		False
to5-alpha-L-Frup.params	segfault					name	False		False
to3-alpha-L-Frup.params	segfault					name	False		False
to1-alpha-L-Frup.params	segfault					name	False		False
to3-beta-D-Frup.params	segfault					name	False		False
to5-beta-L-Frup.params	segfault					name	False		False
to1-beta-D-Frup.params	segfault					name	False		False
to4-alpha-D-Fruf.params	segfault					name	False		False
to3-alpha-D-Frup.params	segfault					name	False		False
to3-beta-L-Frup.params	segfault					name	False		False
to1-alpha-D-Frup.params	segfault					name	False		False
to4-beta-D-Fruf.params	segfault					name	False		False
to4-beta-D-Frup.params	segfault					name	False		False
to5-alpha-D-Frup.params	segfault					name	False		False
to4-alpha-D-Frup.params	segfault					name	False		False
to5-beta-L-Tagp.params	segfault					name	False		False
to1-beta-D-Tagp.params	segfault					name	False		False
to5-alpha-D-Tagp.params	segfault					name	False		False
to4-alpha-D-Tagp.params	segfault					name	False		False
to4-beta-D-Tagp.params	segfault					name	False		False
to3-beta-L-Tagp.params	segfault					name	False		False
to1-alpha-D-Tagp.params	segfault					name	False		False
to3-alpha-D-Tagp.params	segfault					name	False		False
to1-beta-L-Tagp.params	segfault					name	False		False
to5-beta-D-Tagp.params	segfault					name	False		False
to1-alpha-L-Tagp.params	segfault					name	False		False
to3-beta-D-Tagp.params	segfault					name	False		False
to3-alpha-L-Tagp.params	segfault					name	False		False
to4-alpha-L-Tagp.params	segfault					name	False		False
to5-alpha-L-Tagp.params	segfault					name	False		False
to4-beta-L-Tagp.params	segfault					name	False		False
to4-alpha-D-Rulf.params	segfault					name	False		False
to4-beta-D-Rulf.params	segfault					name	False		False
to1-alpha-D-Rulf.params	segfault					name	False		False
to3-beta-L-Rulf.params	segfault					name	False		False
to3-alpha-D-Rulf.params	segfault					name	False		False
to1-beta-D-Rulf.params	segfault					name	False		False
to3-beta-D-Rulf.params	segfault					name	False		False
to1-alpha-L-Rulf.params	segfault					name	False		False
to3-alpha-L-Rulf.params	segfault					name	False		False
to4-alpha-L-Rulf.params	segfault					name	False		False
to4-beta-L-Rulf.params	segfault					name	False		False
to1-beta-L-Rulf.params	segfault					name	False		False
to1-beta-D-Xulf.params	segfault					name	False		False
to3-alpha-D-Xulf.params	segfault					name	False		False
to3-beta-L-Xulf.params	segfault					name	False		False
to1-alpha-D-Xulf.params	segfault					name	False		False
to4-beta-D-Xulf.params	segfault					name	False		False
to4-alpha-D-Xulf.params	segfault					name	False		False
to1-beta-L-Xulf.params	segfault					name	False		False
to4-beta-L-Xulf.params	segfault					name	False		False
to4-alpha-L-Xulf.params	segfault					name	False		False
to3-alpha-L-Xulf.params	segfault					name	False		False
to1-alpha-L-Xulf.params	segfault					name	False		False
to3-beta-D-Xulf.params	segfault					name	False		False
to8-alpha-Kdnp.params	segfault					name	False		False
to4-beta-Neup.params	segfault					name	False		False
to9-alpha-Kdnp.params	segfault					name	False		False
to5-beta-Kdnp.params	segfault					name	False		False
to9-alpha-Neup.params	segfault					name	False		False
to8-alpha-Neup.params	segfault					name	False		False
to4-beta-Kdnp.params	segfault					name	False		False
to7-alpha-Kdnp.params	segfault					name	False		False
to4-alpha-Neup.params	segfault					name	False		False
to8-beta-Kdnp.params	segfault					name	False		False
to9-beta-Neup.params	segfault					name	False		False
to7-beta-Kdnp.params	segfault					name	False		False
to5-alpha-Kdnp.params	segfault					name	False		False
to7-beta-Neup.params	segfault					name	False		False
to9-beta-Kdnp.params	segfault					name	False		False
to4-alpha-Kdnp.params	segfault					name	False		False
to7-alpha-Neup.params	segfault					name	False		False
to8-beta-Neup.params	segfault					name	False		False
D-Gly.params	segfault					name	False		False
L-Gly.params	segfault					name	False		False
to2-beta-L-Thrf.params	segfault					name	False		False
to2-alpha-L-Thrf.params	segfault					name	False		False
to3-alpha-L-Thrf.params	segfault					name	False		False
to3-beta-D-Thrf.params	segfault					name	False		False
to2-beta-D-Thrf.params	segfault					name	False		False
to3-alpha-D-Thrf.params	segfault					name	False		False
to2-alpha-D-Thrf.params	segfault					name	False		False
to3-beta-L-Thrf.params	segfault					name	False		False
to2-beta-L-Eryf.params	segfault					name	False		False
to3-beta-D-Eryf.params	segfault					name	False		False
to2-alpha-L-Eryf.params	segfault					name	False		False
to3-alpha-L-Eryf.params	segfault					name	False		False
to2-beta-D-Eryf.params	segfault					name	False		False
to3-beta-L-Eryf.params	segfault					name	False		False
to3-alpha-D-Eryf.params	segfault					name	False		False
to2-alpha-D-Eryf.params	segfault					name	False		False
to3-alpha-L-Altp.params	segfault					name	False		False
to5-alpha-L-Altf.params	segfault					name	False		False
to4-alpha-D-Digp.params	segfault					name	False		False
to3-alpha-D-Digf.params	segfault					name	False		False
to2-alpha-L-Altp.params	segfault					name	False		False
to3-beta-L-Digf.params	segfault					name	False		False
to3-beta-D-Altp.params	segfault					name	False		False
to6-alpha-L-Altf.params	segfault					name	False		False
to4-beta-D-Digp.params	segfault					name	False		False
to6-alpha-L-Altp.params	segfault					name	False		False
to3-beta-D-Altf.params	segfault					name	False		False
to4-beta-L-Altp.params	segfault					name	False		False
to3-beta-L-Digp.params	segfault					name	False		False
to4-alpha-L-Altp.params	segfault					name	False		False
to5-alpha-D-Digf.params	segfault					name	False		False
to2-alpha-L-Altf.params	segfault					name	False		False
to3-alpha-D-Digp.params	segfault					name	False		False
to3-alpha-L-Altf.params	segfault					name	False		False
to5-beta-D-Altf.params	segfault					name	False		False
to6-beta-D-Altp.params	segfault					name	False		False
to2-beta-L-Altp.params	segfault					name	False		False
to2-beta-L-Altf.params	segfault					name	False		False
to5-beta-L-Digf.params	segfault					name	False		False
to6-beta-D-Altf.params	segfault					name	False		False
to4-beta-D-Altp.params	segfault					name	False		False
to3-beta-D-Digp.params	segfault					name	False		False
to6-alpha-D-Altp.params	segfault					name	False		False
to3-beta-L-Altf.params	segfault					name	False		False
to3-alpha-D-Altf.params	segfault					name	False		False
to4-alpha-D-Altp.params	segfault					name	False		False
to5-alpha-L-Digf.params	segfault					name	False		False
to2-alpha-D-Altf.params	segfault					name	False		False
to3-alpha-L-Digp.params	segfault					name	False		False
to3-alpha-L-Digf.params	segfault					name	False		False
to2-alpha-D-Altp.params	segfault					name	False		False
to3-alpha-D-Altp.params	segfault					name	False		False
to5-alpha-D-Altf.params	segfault					name	False		False
to4-alpha-L-Digp.params	segfault					name	False		False
to3-beta-L-Altp.params	segfault					name	False		False
to6-alpha-D-Altf.params	segfault					name	False		False
to4-beta-L-Digp.params	segfault					name	False		False
to3-beta-D-Digf.params	segfault					name	False		False
to6-beta-L-Altf.params	segfault					name	False		False
to2-beta-D-Altf.params	segfault					name	False		False
to5-beta-D-Digf.params	segfault					name	False		False
to2-beta-D-Altp.params	segfault					name	False		False
to5-beta-L-Altf.params	segfault					name	False		False
to6-beta-L-Altp.params	segfault					name	False		False
to2-beta-D-Idof.params	segfault					name	False		False
to6-beta-L-Idof.params	segfault					name	False		False
to6-beta-L-Idop.params	segfault					name	False		False
to5-beta-L-Idof.params	segfault					name	False		False
to2-beta-D-Idop.params	segfault					name	False		False
to2-alpha-D-Idof.params	segfault					name	False		False
to4-alpha-D-Idop.params	segfault					name	False		False
to3-alpha-D-Idof.params	segfault					name	False		False
to3-beta-L-Idof.params	segfault					name	False		False
to6-alpha-D-Idop.params	segfault					name	False		False
to4-beta-D-Idop.params	segfault					name	False		False
to6-alpha-D-Idof.params	segfault					name	False		False
to3-beta-L-Idop.params	segfault					name	False		False
to5-alpha-D-Idof.params	segfault					name	False		False
to3-alpha-D-Idop.params	segfault					name	False		False
to2-alpha-D-Idop.params	segfault					name	False		False
to2-beta-L-Idop.params	segfault					name	False		False
to6-beta-D-Idop.params	segfault					name	False		False
to5-beta-D-Idof.params	segfault					name	False		False
to6-beta-D-Idof.params	segfault					name	False		False
to2-beta-L-Idof.params	segfault					name	False		False
to6-alpha-L-Idof.params	segfault					name	False		False
to3-beta-D-Idop.params	segfault					name	False		False
to2-alpha-L-Idop.params	segfault					name	False		False
to5-alpha-L-Idof.params	segfault					name	False		False
to3-alpha-L-Idop.params	segfault					name	False		False
to3-alpha-L-Idof.params	segfault					name	False		False
to2-alpha-L-Idof.params	segfault					name	False		False
to4-alpha-L-Idop.params	segfault					name	False		False
to4-beta-L-Idop.params	segfault					name	False		False
to3-beta-D-Idof.params	segfault					name	False		False
to6-alpha-L-Idop.params	segfault					name	False		False
to2-alpha-D-Talp.params	segfault					name	False		False
to5-alpha-D-Talf.params	segfault					name	False		False
to3-alpha-D-Talp.params	segfault					name	False		False
to6-alpha-D-Talf.params	segfault					name	False		False
to3-beta-L-Talp.params	segfault					name	False		False
to4-beta-D-Talp.params	segfault					name	False		False
to3-beta-L-Talf.params	segfault					name	False		False
to6-alpha-D-Talp.params	segfault					name	False		False
to3-alpha-D-Talf.params	segfault					name	False		False
to2-alpha-D-Talf.params	segfault					name	False		False
to4-alpha-D-Talp.params	segfault					name	False		False
to2-beta-D-Talp.params	segfault					name	False		False
to6-beta-L-Talp.params	segfault					name	False		False
to5-beta-L-Talf.params	segfault					name	False		False
to6-beta-L-Talf.params	segfault					name	False		False
to2-beta-D-Talf.params	segfault					name	False		False
to3-beta-D-Talf.params	segfault					name	False		False
to6-alpha-L-Talp.params	segfault					name	False		False
to4-beta-L-Talp.params	segfault					name	False		False
to2-alpha-L-Talf.params	segfault					name	False		False
to4-alpha-L-Talp.params	segfault					name	False		False
to3-alpha-L-Talf.params	segfault					name	False		False
to5-alpha-L-Talf.params	segfault					name	False		False
to3-alpha-L-Talp.params	segfault					name	False		False
to2-alpha-L-Talp.params	segfault					name	False		False
to6-alpha-L-Talf.params	segfault					name	False		False
to3-beta-D-Talp.params	segfault					name	False		False
to2-beta-L-Talf.params	segfault					name	False		False
to6-beta-D-Talf.params	segfault					name	False		False
to6-beta-D-Talp.params	segfault					name	False		False
to5-beta-D-Talf.params	segfault					name	False		False
to2-beta-L-Talp.params	segfault					name	False		False
to3-alpha-D-Quif.params	segfault					name	False		False
to5-beta-L-Olif.params	segfault					name	False		False
to2-alpha-D-Quif.params	segfault					name	False		False
to5-beta-Parf.params	segfault					name	False		False
to3-alpha-Bacp.params	segfault					name	False		False
to6-beta-Murf.params	segfault					name	False		False
to4-alpha-D-Quip.params	segfault					name	False		False
to4-beta-D-Quip.params	segfault					name	False		False
to2-beta-L-Glcp.params	segfault					name	False		False
to3-beta-L-Quif.params	segfault					name	False		False
to5-beta-D-Glcf.params	segfault					name	False		False
to6-beta-D-Glcp.params	segfault					name	False		False
to4-alpha-Murp.params	segfault					name	False		False
to6-beta-D-Glcf.params	segfault					name	False		False
to3-beta-L-Quip.params	segfault					name	False		False
to2-beta-L-Glcf.params	segfault					name	False		False
to5-beta-D-Rhof.params	segfault					name	False		False
to2-alpha-D-Quip.params	segfault					name	False		False
to6-beta-Murp.params	segfault					name	False		False
to5-alpha-D-Quif.params	segfault					name	False		False
to3-beta-Bacp.params	segfault					name	False		False
to5-alpha-Murf.params	segfault					name	False		False
to3-alpha-D-Quip.params	segfault					name	False		False
to2-alpha-L-Glcp.params	segfault					name	False		False
to3-alpha-L-Glcp.params	segfault					name	False		False
to4-alpha-L-Rhop.params	segfault					name	False		False
to5-alpha-L-Glcf.params	segfault					name	False		False
to3-beta-L-Olip.params	segfault					name	False		False
to3-beta-D-Glcp.params	segfault					name	False		False
to4-beta-L-Rhop.params	segfault					name	False		False
to6-alpha-L-Glcf.params	segfault					name	False		False
to5-alpha-D-Olif.params	segfault					name	False		False
to3-alpha-D-Olip.params	segfault					name	False		False
to2-beta-D-Quif.params	segfault					name	False		False
to6-alpha-Murf.params	segfault					name	False		False
to6-alpha-Murp.params	segfault					name	False		False
to2-beta-D-Quip.params	segfault					name	False		False
to4-alpha-D-Olip.params	segfault					name	False		False
to4-beta-L-Glcp.params	segfault					name	False		False
to3-alpha-D-Olif.params	segfault					name	False		False
to5-beta-L-Quif.params	segfault					name	False		False
to6-alpha-L-Glcp.params	segfault					name	False		False
to3-beta-D-Glcf.params	segfault					name	False		False
to3-beta-L-Olif.params	segfault					name	False		False
to3-alpha-L-Glcf.params	segfault					name	False		False
to4-alpha-L-Glcp.params	segfault					name	False		False
to4-beta-Parp.params	segfault					name	False		False
to5-alpha-L-Rhof.params	segfault					name	False		False
to4-beta-D-Olip.params	segfault					name	False		False
to2-alpha-L-Glcf.params	segfault					name	False		False
to2-alpha-Parp.params	segfault					name	False		False
to2-beta-D-Glcf.params	segfault					name	False		False
to5-beta-L-Rhof.params	segfault					name	False		False
to6-beta-L-Glcf.params	segfault					name	False		False
to3-beta-D-Quip.params	segfault					name	False		False
to5-alpha-L-Quif.params	segfault					name	False		False
to3-alpha-L-Quip.params	segfault					name	False		False
to2-alpha-L-Quip.params	segfault					name	False		False
to2-alpha-L-Quif.params	segfault					name	False		False
to4-alpha-L-Quip.params	segfault					name	False		False
to3-alpha-L-Quif.params	segfault					name	False		False
to4-beta-Murp.params	segfault					name	False		False
to5-beta-D-Olif.params	segfault					name	False		False
to3-beta-D-Quif.params	segfault					name	False		False
to5-beta-L-Glcf.params	segfault					name	False		False
to6-beta-L-Glcp.params	segfault					name	False		False
to4-beta-L-Quip.params	segfault					name	False		False
to2-beta-D-Glcp.params	segfault					name	False		False
to2-alpha-Parf.params	segfault					name	False		False
to3-alpha-L-Olif.params	segfault					name	False		False
to5-beta-D-Quif.params	segfault					name	False		False
to6-alpha-D-Glcp.params	segfault					name	False		False
to3-beta-L-Glcf.params	segfault					name	False		False
to2-beta-L-Quip.params	segfault					name	False		False
to4-alpha-L-Olip.params	segfault					name	False		False
to4-beta-D-Glcp.params	segfault					name	False		False
to4-alpha-D-Glcp.params	segfault					name	False		False
to5-alpha-D-Rhof.params	segfault					name	False		False
to4-beta-L-Olip.params	segfault					name	False		False
to2-alpha-D-Glcf.params	segfault					name	False		False
to5-beta-Murf.params	segfault					name	False		False
to3-beta-D-Olif.params	segfault					name	False		False
to3-alpha-D-Glcf.params	segfault					name	False		False
to2-beta-Parp.params	segfault					name	False		False
to3-alpha-D-Glcp.params	segfault					name	False		False
to2-beta-Parf.params	segfault					name	False		False
to4-alpha-D-Rhop.params	segfault					name	False		False
to5-alpha-D-Glcf.params	segfault					name	False		False
to3-beta-D-Olip.params	segfault					name	False		False
to2-alpha-D-Glcp.params	segfault					name	False		False
to5-alpha-Parf.params	segfault					name	False		False
to2-beta-L-Quif.params	segfault					name	False		False
to4-alpha-Parp.params	segfault					name	False		False
to3-beta-L-Glcp.params	segfault					name	False		False
to4-beta-D-Rhop.params	segfault					name	False		False
to5-alpha-L-Olif.params	segfault					name	False		False
to6-alpha-D-Glcf.params	segfault					name	False		False
to3-alpha-L-Olip.params	segfault					name	False		False
to3-alpha-D-Gulp.params	segfault					name	False		False
to5-alpha-D-Gulf.params	segfault					name	False		False
to2-alpha-D-Gulp.params	segfault					name	False		False
to6-alpha-D-Gulf.params	segfault					name	False		False
to3-beta-L-Gulp.params	segfault					name	False		False
to3-beta-L-Gulf.params	segfault					name	False		False
to6-alpha-D-Gulp.params	segfault					name	False		False
to4-beta-D-Gulp.params	segfault					name	False		False
to4-alpha-D-Gulp.params	segfault					name	False		False
to2-alpha-D-Gulf.params	segfault					name	False		False
to3-alpha-D-Gulf.params	segfault					name	False		False
to5-beta-L-Gulf.params	segfault					name	False		False
to6-beta-L-Gulp.params	segfault					name	False		False
to2-beta-D-Gulp.params	segfault					name	False		False
to2-beta-D-Gulf.params	segfault					name	False		False
to6-beta-L-Gulf.params	segfault					name	False		False
to4-beta-L-Gulp.params	segfault					name	False		False
to3-beta-D-Gulf.params	segfault					name	False		False
to6-alpha-L-Gulp.params	segfault					name	False		False
to3-alpha-L-Gulf.params	segfault					name	False		False
to4-alpha-L-Gulp.params	segfault					name	False		False
to2-alpha-L-Gulf.params	segfault					name	False		False
to2-alpha-L-Gulp.params	segfault					name	False		False
to3-alpha-L-Gulp.params	segfault					name	False		False
to5-alpha-L-Gulf.params	segfault					name	False		False
to6-alpha-L-Gulf.params	segfault					name	False		False
to3-beta-D-Gulp.params	segfault					name	False		False
to6-beta-D-Gulf.params	segfault					name	False		False
to2-beta-L-Gulf.params	segfault					name	False		False
to2-beta-L-Gulp.params	segfault					name	False		False
to5-beta-D-Gulf.params	segfault					name	False		False
to6-beta-D-Gulp.params	segfault					name	False		False
to2-alpha-D-Manf.params	segfault					name	False		False
to4-alpha-D-Manp.params	segfault					name	False		False
to2-beta-D-Rhap.params	segfault					name	False		False
to3-alpha-D-Manf.params	segfault					name	False		False
to5-beta-L-Rhaf.params	segfault					name	False		False
to3-beta-L-Manf.params	segfault					name	False		False
to6-alpha-D-Manp.params	segfault					name	False		False
to4-beta-D-Manp.params	segfault					name	False		False
to6-alpha-D-Manf.params	segfault					name	False		False
to3-beta-L-Manp.params	segfault					name	False		False
to5-alpha-D-Manf.params	segfault					name	False		False
to3-alpha-D-Manp.params	segfault					name	False		False
to5-beta-Tyvf.params	segfault					name	False		False
to2-beta-D-Rhaf.params	segfault					name	False		False
to2-alpha-D-Manp.params	segfault					name	False		False
to3-beta-L-Rhap.params	segfault					name	False		False
to4-beta-Tyvp.params	segfault					name	False		False
to2-beta-D-Manf.params	segfault					name	False		False
to2-alpha-D-Rhap.params	segfault					name	False		False
to5-alpha-D-Rhaf.params	segfault					name	False		False
to3-alpha-D-Rhap.params	segfault					name	False		False
to6-beta-L-Manf.params	segfault					name	False		False
to6-beta-L-Manp.params	segfault					name	False		False
to3-alpha-D-Rhaf.params	segfault					name	False		False
to5-beta-L-Manf.params	segfault					name	False		False
to2-alpha-D-Rhaf.params	segfault					name	False		False
to4-alpha-D-Rhap.params	segfault					name	False		False
to2-beta-D-Manp.params	segfault					name	False		False
to4-beta-D-Rhap.params	segfault					name	False		False
to3-beta-L-Rhaf.params	segfault					name	False		False
to6-alpha-L-Manf.params	segfault					name	False		False
to3-beta-D-Manp.params	segfault					name	False		False
to2-alpha-Tyvf.params	segfault					name	False		False
to2-beta-L-Rhaf.params	segfault					name	False		False
to2-alpha-L-Manp.params	segfault					name	False		False
to5-alpha-L-Manf.params	segfault					name	False		False
to3-alpha-L-Manp.params	segfault					name	False		False
to3-alpha-L-Manf.params	segfault					name	False		False
to5-beta-D-Rhaf.params	segfault					name	False		False
to2-alpha-L-Manf.params	segfault					name	False		False
to4-alpha-L-Manp.params	segfault					name	False		False
to2-beta-L-Rhap.params	segfault					name	False		False
to2-alpha-Tyvp.params	segfault					name	False		False
to4-beta-L-Manp.params	segfault					name	False		False
to3-beta-D-Manf.params	segfault					name	False		False
to6-alpha-L-Manp.params	segfault					name	False		False
to4-alpha-Tyvp.params	segfault					name	False		False
to2-alpha-L-Rhaf.params	segfault					name	False		False
to4-alpha-L-Rhap.params	segfault					name	False		False
to2-beta-L-Manp.params	segfault					name	False		False
to6-beta-D-Manp.params	segfault					name	False		False
to3-alpha-L-Rhaf.params	segfault					name	False		False
to5-beta-D-Manf.params	segfault					name	False		False
to2-beta-Tyvf.params	segfault					name	False		False
to3-beta-D-Rhaf.params	segfault					name	False		False
to4-beta-L-Rhap.params	segfault					name	False		False
to5-alpha-Tyvf.params	segfault					name	False		False
to2-beta-Tyvp.params	segfault					name	False		False
to3-beta-D-Rhap.params	segfault					name	False		False
to5-alpha-L-Rhaf.params	segfault					name	False		False
to3-alpha-L-Rhap.params	segfault					name	False		False
to6-beta-D-Manf.params	segfault					name	False		False
to2-beta-L-Manf.params	segfault					name	False		False
to2-alpha-L-Rhap.params	segfault					name	False		False
to2-beta-D-Allf.params	segfault					name	False		False
to6-beta-L-Allf.params	segfault					name	False		False
to5-beta-L-Allf.params	segfault					name	False		False
to6-beta-L-Allp.params	segfault					name	False		False
to2-beta-D-Allp.params	segfault					name	False		False
to4-alpha-D-Allp.params	segfault					name	False		False
to2-alpha-D-Allf.params	segfault					name	False		False
to3-alpha-D-Allf.params	segfault					name	False		False
to6-alpha-D-Allp.params	segfault					name	False		False
to3-beta-L-Allf.params	segfault					name	False		False
to4-beta-D-Allp.params	segfault					name	False		False
to3-beta-L-Allp.params	segfault					name	False		False
to6-alpha-D-Allf.params	segfault					name	False		False
to3-alpha-D-Allp.params	segfault					name	False		False
to5-alpha-D-Allf.params	segfault					name	False		False
to2-alpha-D-Allp.params	segfault					name	False		False
to2-beta-L-Allp.params	segfault					name	False		False
to5-beta-D-Allf.params	segfault					name	False		False
to6-beta-D-Allp.params	segfault					name	False		False
to6-beta-D-Allf.params	segfault					name	False		False
to2-beta-L-Allf.params	segfault					name	False		False
to3-beta-D-Allp.params	segfault					name	False		False
to6-alpha-L-Allf.params	segfault					name	False		False
to2-alpha-L-Allp.params	segfault					name	False		False
to3-alpha-L-Allp.params	segfault					name	False		False
to5-alpha-L-Allf.params	segfault					name	False		False
to3-alpha-L-Allf.params	segfault					name	False		False
to4-alpha-L-Allp.params	segfault					name	False		False
to2-alpha-L-Allf.params	segfault					name	False		False
to4-beta-L-Allp.params	segfault					name	False		False
to6-alpha-L-Allp.params	segfault					name	False		False
to3-beta-D-Allf.params	segfault					name	False		False
to4-beta-D-Galp.params	segfault					name	False		False
to5-beta-D-Fucf.params	segfault					name	False		False
to3-beta-L-Galf.params	segfault					name	False		False
to6-alpha-D-Galp.params	segfault					name	False		False
to3-alpha-D-Daup.params	segfault					name	False		False
to5-alpha-D-Dauf.params	segfault					name	False		False
to2-beta-L-Fucp.params	segfault					name	False		False
to3-beta-L-Daup.params	segfault					name	False		False
to3-alpha-D-Galf.params	segfault					name	False		False
to2-alpha-D-Galf.params	segfault					name	False		False
to5-beta-L-Colf.params	segfault					name	False		False
to4-alpha-D-Galp.params	segfault					name	False		False
to4-alpha-Daup.params	segfault					name	False		False
to4-beta-D-Daup.params	segfault					name	False		False
to2-alpha-D-Galp.params	segfault					name	False		False
to5-alpha-D-Galf.params	segfault					name	False		False
to3-beta-L-Dauf.params	segfault					name	False		False
to3-alpha-D-Galp.params	segfault					name	False		False
to2-beta-L-Fucf.params	segfault					name	False		False
to6-alpha-D-Galf.params	segfault					name	False		False
to3-beta-L-Galp.params	segfault					name	False		False
to3-alpha-D-Dauf.params	segfault					name	False		False
to4-alpha-D-Daup.params	segfault					name	False		False
to6-beta-L-Galf.params	segfault					name	False		False
to2-beta-D-Galf.params	segfault					name	False		False
to3-beta-D-Fucp.params	segfault					name	False		False
to5-alpha-L-Fucf.params	segfault					name	False		False
to3-alpha-L-Fucp.params	segfault					name	False		False
to5-beta-L-Dauf.params	segfault					name	False		False
to5-beta-D-Abef.params	segfault					name	False		False
to2-alpha-L-Fucp.params	segfault					name	False		False
to2-alpha-L-Fucf.params	segfault					name	False		False
to4-alpha-L-Fucp.params	segfault					name	False		False
to3-alpha-L-Fucf.params	segfault					name	False		False
to3-beta-D-Fucf.params	segfault					name	False		False
to2-beta-D-Galp.params	segfault					name	False		False
to4-beta-L-Fucp.params	segfault					name	False		False
to6-beta-L-Galp.params	segfault					name	False		False
to5-beta-L-Galf.params	segfault					name	False		False
to5-alpha-L-Galf.params	segfault					name	False		False
to3-beta-D-Dauf.params	segfault					name	False		False
to2-beta-L-Colf.params	segfault					name	False		False
to3-alpha-L-Galp.params	segfault					name	False		False
to4-beta-L-Daup.params	segfault					name	False		False
to2-alpha-L-Galp.params	segfault					name	False		False
to4-beta-D-Abep.params	segfault					name	False		False
to4-alpha-D-Abep.params	segfault					name	False		False
to4-alpha-L-Daup.params	segfault					name	False		False
to2-alpha-D-Abef.params	segfault					name	False		False
to2-beta-D-Fucf.params	segfault					name	False		False
to6-alpha-L-Galf.params	segfault					name	False		False
to3-beta-D-Galp.params	segfault					name	False		False
to3-alpha-L-Dauf.params	segfault					name	False		False
to3-beta-D-Galf.params	segfault					name	False		False
to6-alpha-L-Galp.params	segfault					name	False		False
to3-alpha-L-Daup.params	segfault					name	False		False
to2-beta-D-Fucp.params	segfault					name	False		False
to5-alpha-L-Dauf.params	segfault					name	False		False
to5-alpha-D-Abef.params	segfault					name	False		False
to4-beta-L-Galp.params	segfault					name	False		False
to2-alpha-D-Abep.params	segfault					name	False		False
to5-beta-L-Fucf.params	segfault					name	False		False
to2-alpha-L-Galf.params	segfault					name	False		False
to4-alpha-L-Galp.params	segfault					name	False		False
to3-beta-D-Daup.params	segfault					name	False		False
to3-alpha-L-Galf.params	segfault					name	False		False
to2-beta-L-Colp.params	segfault					name	False		False
to3-alpha-D-Fucf.params	segfault					name	False		False
to2-beta-D-Abef.params	segfault					name	False		False
to2-alpha-D-Fucf.params	segfault					name	False		False
to4-beta-L-Colp.params	segfault					name	False		False
to4-alpha-D-Fucp.params	segfault					name	False		False
to4-alpha-L-Colp.params	segfault					name	False		False
to4-beta-D-Fucp.params	segfault					name	False		False
to6-beta-D-Galp.params	segfault					name	False		False
to5-beta-D-Galf.params	segfault					name	False		False
to2-alpha-L-Colf.params	segfault					name	False		False
to3-beta-L-Fucf.params	segfault					name	False		False
to2-beta-L-Galp.params	segfault					name	False		False
to2-beta-L-Galf.params	segfault					name	False		False
to3-beta-L-Fucp.params	segfault					name	False		False
to5-alpha-L-Colf.params	segfault					name	False		False
to2-alpha-L-Colp.params	segfault					name	False		False
to6-beta-D-Galf.params	segfault					name	False		False
to5-beta-D-Dauf.params	segfault					name	False		False
to2-alpha-D-Fucp.params	segfault					name	False		False
to5-alpha-D-Fucf.params	segfault					name	False		False
to2-beta-D-Abep.params	segfault					name	False		False
to3-alpha-D-Fucp.params	segfault					name	False		False
to2-beta-D-Lyxf.params	segfault					name	False		False
to2-beta-D-Lyxp.params	segfault					name	False		False
to5-beta-L-Lyxf.params	segfault					name	False		False
to3-alpha-D-Lyxf.params	segfault					name	False		False
to4-alpha-D-Lyxp.params	segfault					name	False		False
to2-alpha-D-Lyxf.params	segfault					name	False		False
to4-beta-D-Lyxp.params	segfault					name	False		False
to3-beta-L-Lyxf.params	segfault					name	False		False
to3-beta-L-Lyxp.params	segfault					name	False		False
to2-alpha-D-Lyxp.params	segfault					name	False		False
to3-alpha-D-Lyxp.params	segfault					name	False		False
to5-alpha-D-Lyxf.params	segfault					name	False		False
to5-beta-D-Lyxf.params	segfault					name	False		False
to2-beta-L-Lyxp.params	segfault					name	False		False
to2-beta-L-Lyxf.params	segfault					name	False		False
to3-beta-D-Lyxp.params	segfault					name	False		False
to3-alpha-L-Lyxp.params	segfault					name	False		False
to5-alpha-L-Lyxf.params	segfault					name	False		False
to2-alpha-L-Lyxp.params	segfault					name	False		False
to4-alpha-L-Lyxp.params	segfault					name	False		False
to2-alpha-L-Lyxf.params	segfault					name	False		False
to3-alpha-L-Lyxf.params	segfault					name	False		False
to3-beta-D-Lyxf.params	segfault					name	False		False
to4-beta-L-Lyxp.params	segfault					name	False		False
to2-alpha-D-Ribp.params	segfault					name	False		False
to3-alpha-D-Ribp.params	segfault					name	False		False
to5-alpha-D-Ribf.params	segfault					name	False		False
to3-beta-L-Ribp.params	segfault					name	False		False
to4-beta-D-Ribp.params	segfault					name	False		False
to3-beta-L-Ribf.params	segfault					name	False		False
to3-alpha-D-Ribf.params	segfault					name	False		False
to4-alpha-D-Ribp.params	segfault					name	False		False
to2-alpha-D-Ribf.params	segfault					name	False		False
to2-beta-D-Ribp.params	segfault					name	False		False
to5-beta-L-Ribf.params	segfault					name	False		False
to2-beta-D-Ribf.params	segfault					name	False		False
to3-beta-D-Ribf.params	segfault					name	False		False
to4-beta-L-Ribp.params	segfault					name	False		False
to4-alpha-L-Ribp.params	segfault					name	False		False
to2-alpha-L-Ribf.params	segfault					name	False		False
to3-alpha-L-Ribf.params	segfault					name	False		False
to3-alpha-L-Ribp.params	segfault					name	False		False
to5-alpha-L-Ribf.params	segfault					name	False		False
to2-alpha-L-Ribp.params	segfault					name	False		False
to3-beta-D-Ribp.params	segfault					name	False		False
to2-beta-L-Ribf.params	segfault					name	False		False
to5-beta-D-Ribf.params	segfault					name	False		False
to2-beta-L-Ribp.params	segfault					name	False		False
to3-alpha-L-Araf.params	segfault					name	False		False
to2-alpha-L-Araf.params	segfault					name	False		False
to4-alpha-L-Arap.params	segfault					name	False		False
to4-beta-L-Arap.params	segfault					name	False		False
to3-beta-D-Araf.params	segfault					name	False		False
to3-beta-D-Arap.params	segfault					name	False		False
to2-alpha-L-Arap.params	segfault					name	False		False
to5-alpha-L-Araf.params	segfault					name	False		False
to3-alpha-L-Arap.params	segfault					name	False		False
to2-beta-L-Araf.params	segfault					name	False		False
to2-beta-L-Arap.params	segfault					name	False		False
to5-beta-D-Araf.params	segfault					name	False		False
to3-beta-L-Arap.params	segfault					name	False		False
to5-alpha-D-Araf.params	segfault					name	False		False
to3-alpha-D-Arap.params	segfault					name	False		False
to2-alpha-D-Arap.params	segfault					name	False		False
to2-alpha-D-Araf.params	segfault					name	False		False
to4-alpha-D-Arap.params	segfault					name	False		False
to3-alpha-D-Araf.params	segfault					name	False		False
to3-beta-L-Araf.params	segfault					name	False		False
to4-beta-D-Arap.params	segfault					name	False		False
to5-beta-L-Araf.params	segfault					name	False		False
to2-beta-D-Arap.params	segfault					name	False		False
to2-beta-D-Araf.params	segfault					name	False		False
to3-alpha-D-Xylp.params	segfault					name	False		False
to5-alpha-D-Xylf.params	segfault					name	False		False
to2-alpha-D-Xylp.params	segfault					name	False		False
to3-beta-L-Xylp.params	segfault					name	False		False
to3-beta-L-Xylf.params	segfault					name	False		False
to4-beta-D-Xylp.params	segfault					name	False		False
to4-alpha-D-Xylp.params	segfault					name	False		False
to2-alpha-D-Xylf.params	segfault					name	False		False
to3-alpha-D-Xylf.params	segfault					name	False		False
to5-beta-L-Xylf.params	segfault					name	False		False
to2-beta-D-Xylp.params	segfault					name	False		False
to2-beta-D-Xylf.params	segfault					name	False		False
to4-beta-L-Xylp.params	segfault					name	False		False
to3-beta-D-Xylf.params	segfault					name	False		False
to3-alpha-L-Xylf.params	segfault					name	False		False
to4-alpha-L-Xylp.params	segfault					name	False		False
to2-alpha-L-Xylf.params	segfault					name	False		False
to2-alpha-L-Xylp.params	segfault					name	False		False
to3-alpha-L-Xylp.params	segfault					name	False		False
to5-alpha-L-Xylf.params	segfault					name	False		False
to3-beta-D-Xylp.params	segfault					name	False		False
to2-beta-L-Xylf.params	segfault					name	False		False
to2-beta-L-Xylp.params	segfault					name	False		False
to5-beta-D-Xylf.params	segfault					name	False		False
MEM.params	segfault	membrane/MEM.params	MEM	TYPE LIGAND	Rosetta Residue Topology File Type: MEM Desc: Defines the position of the implicit membrane Author: Rebecca Alford (rfalford12@gmail.com) Author: Julia Koehler Leman (julia.koehler1982@gmail.com) Last Modified 9/6/14 Membrane Thickness Membrane Center Membrane Normal dont interact with anyone		True		False
EMB.params	segfault	membrane/EMB.params	EMB	TYPE LIGAND	Rosetta Residue Topology File Type: EMB Desc: Defines the embedding of a molecule in the implicit membrane Author: Rebecca Alford (rfalford12@gmail.com) Author: Julia Koehler Leman (julia.koehler1982@gmail.com) Last Modified 9/6/14 Embedding Depth Embedding Center Embedding Normal dont interact with anyone		True		False
C2X.params	segfault					name	False		False
C3X.params	segfault					name	False		False
R1A.params		spin_labels/R1A.params	R1A	TYPE POLYMER			True	CC1(C)CC(CSSC[C@H](N)CO)C(C)(C)N1O	False
CED.params	segfault					name	False		False
C4X.params	segfault					name	False		False
NTA.params	segfault					name	False		False
2-aminomethyl-phenylalanine.params		l-ncaa/2-aminomethyl-phenylalanine.params	A34	TYPE POLYMER	2-aminomethyl-phenylalanine params file created by Doug Renfrew. Tweaked 12 March 2018 by Vikram K. Mulligan (vmullig@uw.edu).		True	N[C@H](CO)CC1CCCCC1C[NH3+]	False
2-amino-heptanoic_acid.params		l-ncaa/2-amino-heptanoic_acid.params	A33	TYPE POLYMER			True	CCCCC[C@H](N)CO	False
YPN.params	segfault					name	False		False
NVL.params		l-ncaa/NVL.params	NVL	TYPE POLYMER	Norvaline prepared by P. Douglas Renfrew (renfrew@unc.edu) AMW: this is NVA in the PDB.		True	CCC[C@H](N)CO	False
4J5.params	segfault					name	False		False
trifluoro-leucine_ent2.params		l-ncaa/trifluoro-leucine_ent2.params	C94	TYPE POLYMER			True	C[C@@H](C[C@H](N)CO)C(F)(F)F	False
2-amino-2-phenylbutyric_acid.params		l-ncaa/2-amino-2-phenylbutyric_acid.params	A24	TYPE POLYMER			True	CC[C@@](N)(CO)C1CCCCC1	False
4-methyl-phenylalanine.params		l-ncaa/4-methyl-phenylalanine.params	B27	TYPE POLYMER			True	CC1CCC(C[C@H](N)CO)CC1	False
2-allyl-glycine.params		l-ncaa/2-allyl-glycine.params	A20	TYPE POLYMER			True	CCC[C@H](N)CO	False
5-bromo-tryptophan.params	ERROR: add_bond: atom CZ2 and/or BRT don’t exist!	l-ncaa/5-bromo-tryptophan.params	C80	TYPE POLYMER			True		False
alpha-methyl-leucine.params		l-ncaa/alpha-methyl-leucine.params	B57	TYPE POLYMER			True	CC(C)C[C@](C)(N)CO	False
7-methyl-tryptophan.params		l-ncaa/7-methyl-tryptophan.params	C88	TYPE POLYMER			True	CC1CCCC2C(C[C@H](N)CO)CNC12	False
4.5-dihydroxy-isoleucine.params		l-ncaa/4.5-dihydroxy-isoleucine.params	dhI	TYPE POLYMER	4,5-dihydroxy-isoleucine Added by Vikram K. Mulligan, 10 March 2014, for modelling alpha-amanitin. Modified from ILE.params. residue type Gamma hydroxyl oxygen atom Gamma hydroxyl’s proton ATOM 2HG1 Hapo HA 0.09 0.000 Delta hydroxyl oxygen atom Delta hydroxyl’s proton ATOM 3HD1 Hapo HA 0.09 0.000 BOND CG1 2HG1 BOND CD1 3HD1 APL O to CB distance; max observed in ubiquitin Torsion/angle/distance measured from 1k83 structure. Torsion/angle/distance based on hydroxyl of serine. ICOOR_INTERNAL 3HD1 120.044632 70.500000 1.089057 CD1 CG1 2HD1 Torsion/angle/distance measured from 1k83 structure. Torsion/angle/distance based on hydroxyl of serine. ICOOR_INTERNAL 2HG1 117.500000 70.500000 1.090337 CG1 CB 1HG1		True	C[C@@H]1[C@@H](CO)NOC[C@@H]1O	False
homocysteine.params		l-ncaa/homocysteine.params	C26	TYPE POLYMER			True	N[C@H](CO)CCS	False
2-amino-5-phenyl-pentanoic_acid.params		l-ncaa/2-amino-5-phenyl-pentanoic_acid.params	A31	TYPE POLYMER			True	N[C@H](CO)CCCC1CCCCC1	False
0TD.params	segfault					name	False		False
4-amino-tetrahydrothiopyran-4-carboxylic_acid.params		l-ncaa/4-amino-tetrahydrothiopyran-4-carboxylic_acid.params	B06	TYPE POLYMER	true NU 6 is across the CUT_BOND ICOOR_INTERNAL CB2 71.593205 69.217655 1.541828 CA N LOWER ICOOR_INTERNAL CB2 -24.000000 69.217655 1.541828 CA N LOWER ICOOR_INTERNAL CB2 -84.000000 69.217655 1.541828 CA N LOWER ICOOR_INTERNAL CB2 -124.000000 69.217655 1.541828 CA N LOWER ICOOR_INTERNAL CG2 59.901852 66.372845 1.527240 CB2 CA N ICOOR_INTERNAL SD 62.412721 67.128122 1.814872 CG2 CB2 CA ICOOR_INTERNAL CG1 -53.843574 81.979932 1.813136 SD CG2 CB2 ICOOR_INTERNAL CB1 52.377765 66.823933 1.528880 CG1 SD CG2 ICOOR_INTERNAL VCB1 59.141809 67.349267 1.528583 CA N LOWER ICOOR_INTERNAL VCA 59.141809 67.349267 1.528583 CB1 CG1 SD ICOOR_INTERNAL O -47.912766 61.295150 1.202795 C CA N Fake chi to trick packer		True	NC1(CO)CCSCC1	False
beta-chloro-alanine.params		l-ncaa/beta-chloro-alanine.params	B97	TYPE POLYMER			True	N[C@H](CO)CCl	False
alpha-methyl-phenylalanine.params		l-ncaa/alpha-methyl-phenylalanine.params	B58	TYPE POLYMER			True	C[C@@](N)(CO)CC1CCCCC1	False
V02.params		l-ncaa/V02.params	V02	TYPE POLYMER			True	N[C@H](CO)C1CCC(O)CC1	False
4-fluoro-proline.params_rot		l-ncaa/4-fluoro-proline.params_rot	B19	TYPE POLYMER			True	OC[C@@H]1C[C@@H](F)CN1	False
beta-cyclohexyl-alanine.params		l-ncaa/beta-cyclohexyl-alanine.params	C00	TYPE POLYMER	true NU 6 is across the CUT_BOND must build from end of ring, unlike CB build as branch from mc, unlike CG1		True	N[C@H](CO)CC1CCCCC1	False
4-fluoro-tryptophan.params	segfault					name	False		False
3-hydroxy-tyrosine.params		l-ncaa/3-hydroxy-tyrosine.params	A80	TYPE POLYMER			True	N[C@H](CO)CC1CCC(O)C(O)C1	False
NLU.params		l-ncaa/NLU.params	NLU	TYPE POLYMER	Norleucine – MADE BY BEN STRANGES ROTAMER_AA MET		True	CCCC[C@H](N)CO	False
5-hydroxy-tryptophan.params		l-ncaa/5-hydroxy-tryptophan.params	B36	TYPE POLYMER			True	N[C@H](CO)CC1CNC2CCC(O)CC12	False
beta.beta-diphenyl-alanine.params		l-ncaa/beta.beta-diphenyl-alanine.params	B96	TYPE POLYMER	Beta,beta-diphenyl-alanine params file, created by Doug Renfrew. Tweaked by Vikram K. Mulligan (vmullig@uw.edu) on 12 March 2018.		True	N[C@H](CO)C(C1CCCCC1)C1CCCCC1	False
homophenylalanine.params		l-ncaa/homophenylalanine.params	C27	TYPE POLYMER	Homophenylalanine params file added by Doug Renfrew. Tweaked 12 March 2018 by Vikram K. Mulligan (vmullig@uw.edu).		True	N[C@H](CO)CCC1CCCCC1	False
alpha-methyl-3-hydroxy-tyrosine.params		l-ncaa/alpha-methyl-3-hydroxy-tyrosine.params	B54	TYPE POLYMER			True	C[C@@](N)(CO)CC1CCC(O)C(O)C1	False
homoserine.params		l-ncaa/homoserine.params	C30	TYPE POLYMER			True	N[C@H](CO)CCO	False
alpha-methyl-tyrosine.params		l-ncaa/alpha-methyl-tyrosine.params	B61	TYPE POLYMER			True	C[C@@](N)(CO)CC1CCC(O)CC1	False
2-amino-3-methylamino-propanoic_acid.params	segfault					name	False		False
beta-hydroxy-norvaline.params		l-ncaa/beta-hydroxy-norvaline.params	C04	TYPE POLYMER			True	CC[C@H](O)[C@H](N)CO	False
HIP.params		l-ncaa/HIP.params	HIP	TYPE POLYMER	rosetta residue topology file residue type APL CB to sidechain heavy atom disance – max observed on residue 74 of ubiquitin		True	N[C@H](CO)C[C@H]1CNCN1[PH](O)(O)O	False
3-methyl-histidine.params		l-ncaa/3-methyl-histidine.params	A82	TYPE POLYMER			True	CN1CNCC1C[C@H](N)CO	False
2-amino-4-bromo-4-pentenoic_acid.params	segfault					name	False		False
V04.params		l-ncaa/V04.params	V04	TYPE POLYMER			True	N[C@H](CO)[C@H](O)C1CCC(O)C(Cl)C1	False
5-fluoro-tryptophan.params		l-ncaa/5-fluoro-tryptophan.params	B35	TYPE POLYMER			True	N[C@H](CO)CC1CNC2CCC(F)CC12	False
2.4-diaminobutyric_acid.params		l-ncaa/2.4-diaminobutyric_acid.params	DAB	TYPE POLYMER	2,4-diaminobutyric acid (DAB), commonly called “stubby stubby lysine”. Probably initially added by Doug Renfrew. Params file updated 7 March 2017 by Vikram K. Mulligan (vmullig@uw.edu).		True	N[C@H](CO)CC[NH3+]	False
4-fluoro-proline_puck.params_rot		l-ncaa/4-fluoro-proline_puck.params_rot	C89	TYPE POLYMER			True	OC[C@@H]1C[C@H](F)CN1	False
HLU.params		l-ncaa/HLU.params	HLU	TYPE POLYMER	made by Ben Stranges		True	CC(C)CC[C@H](N)CO	False
2-amino-octanoic_acid.params		l-ncaa/2-amino-octanoic_acid.params	A32	TYPE POLYMER	Use 2-amino-heptanoic acid rotlib for first 4 chi angles, extra chi for the rest		True	CCCCCC[C@H](N)CO	False
alpha-amino-glycine.params		l-ncaa/alpha-amino-glycine.params	B50	TYPE POLYMER			True	N[C@@H]([NH3+])CO	False
beta-beta-dicyclohexyl-alanine.params		l-ncaa/beta-beta-dicyclohexyl-alanine.params	B95	TYPE POLYMER	CUT_BOND CD1 CG1 CUT_BOND CD3 CG2 true NU 6 is across the CUT_BOND true NU 6 is across the CUT_BOND ICOOR_INTERNAL VCG1 -55.2 67.6 1.54023 CD1 CE1 CZ1 build from end of ring, unlike CB ICOOR_INTERNAL VCD1 -172.569 67.852 1.54023 CG1 CB CA build as branch from mc, unlike CG1 must build from end of ring, unlike CB build as branch from mc, unlike CG1 ICOOR_INTERNAL VCG2 -55.2 67.6 1.54023 CD3 CE3 CZ2 must build from end of ring, unlike CB ICOOR_INTERNAL VCD3 -172.569 67.852 1.54023 CG2 CB CA build as branch from mc, unlike CD3 must build from end of ring, unlike CB build as branch from mc, unlike CD3		True	N[C@H](CO)C(C1CCCCC1)C1CCCCC1	False
2-hydroxy-phenylalanine.params		l-ncaa/2-hydroxy-phenylalanine.params	A43	TYPE POLYMER			True	N[C@H](CO)CC1CCCCC1O	False
S56.params		l-ncaa/S56.params	S56	TYPE POLYMER			True	CC(O)N[C@H]1[C@H](O[C@@H]2[C@@H](CO)O[C@@H](NC(O)C[C@H](N)CO)[C@H](NC(C)O)[C@H]2O)O[C@H](CO)[C@@H](O[C@@H]2O[C@H](CO[C@H]3O[C@H](CO)[C@@H](O)[C@H](O[C@H]4O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]4O)[C@@H]3O)[C@@H](O)[C@H](O[C@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]3O)[C@@H]2O)[C@@H]1O	False
hexafluoro-leucine.params		l-ncaa/hexafluoro-leucine.params	C93	TYPE POLYMER			True	N[C@H](CO)CC(C(F)(F)F)C(F)(F)F	False
ethionine.params		l-ncaa/ethionine.params	C20	TYPE POLYMER			True	CCSCC[C@H](N)CO	False
beta-(2-naphthyl)-alanine.params		l-ncaa/beta-(2-naphthyl)-alanine.params	B74	TYPE POLYMER	Beta-(2-naphthyl)-alanine params file by Doug Renfrew. Tweaked 12 March 2018 by Vikram K. Mulligan (vmullig@uw.edu).		True	N[C@H](CO)CC1CCC2CCCCC2C1	False
tert-butyl-glycine.params		l-ncaa/tert-butyl-glycine.params	C55	TYPE POLYMER			True	CC(C)(C)[C@H](N)CO	False
9-anthryl-alanine.params		l-ncaa/9-anthryl-alanine.params	B44	TYPE POLYMER	9-anthryl-alanine params file by Doug Renfrew. Tweaked 12 March 2018 by Vikram K. Mulligan (vmullig@uw.edu).		True	N[C@H](CO)CC1C2CCCCC2CC2CCCCC21	False
6-chloro-tryptophan.params		l-ncaa/6-chloro-tryptophan.params	C84	TYPE POLYMER			True	N[C@H](CO)CC1CNC2CC(Cl)CCC12	False
fluoro-leucine_ent2.params		l-ncaa/fluoro-leucine_ent2.params	C92	TYPE POLYMER			True	C[C@@H](CF)C[C@H](N)CO	False
alpha-methyl-valine.params		l-ncaa/alpha-methyl-valine.params	B62	TYPE POLYMER			True	CC(C)[C@](C)(N)CO	False
penicillamine.params		l-ncaa/penicillamine.params	C41	TYPE POLYMER			True	CC(C)(S)[C@H](N)CO	False
ABA.params		l-ncaa/ABA.params	ABA	TYPE POLYMER	made by Ben Stranges		True	CC[C@H](N)CO	False
4-phenyl-phenylalanine_tyr_rot.params	segfault					name	False		False
4-amino-piperidine-4-carboxylic-acid.params		l-ncaa/4-amino-piperidine-4-carboxylic-acid.params	A98	TYPE POLYMER	true NU 6 is across the CUT_BOND ICOOR_INTERNAL VCB1 59.141809 67.349267 1.528583 CA N LOWER ICOOR_INTERNAL VCA 59.141809 67.349267 1.528583 CB1 CG1 ND Fake chi to trick packer		True	NC1(CO)CC[NH2+]CC1	False
3-methyl-histidine_prot.params		l-ncaa/3-methyl-histidine_prot.params	A83	TYPE POLYMER			True	CN1CNCC1C[C@H](N)CO	False
alpha-methyl-proline.params		l-ncaa/alpha-methyl-proline.params	B59	TYPE POLYMER			True	C[C@@]1(CO)CCCN1	False
alpha-methyl-histidine.params		l-ncaa/alpha-methyl-histidine.params	B56	TYPE POLYMER			True	C[C@@](N)(CO)CC1CNCN1	False
2-indanyl-glycine_puck2.params		l-ncaa/2-indanyl-glycine_puck2.params	A45	TYPE POLYMER	AMW: note that we can’t use A44 for the other pucker anymore because that collides with a real RNA residue we care about So, let’s make the nu torsion sampling system handle this pucker so that we don’t need IGL (former A44) and also A45 (that is aesthetics-defying).		True	N[C@H](CO)C1CC2CCCCC2C1	False
MPH.params	segfault					name	False		False
diphenylglycine.params		l-ncaa/diphenylglycine.params	C15	TYPE POLYMER			True	NC(CO)(C1CCCCC1)C1CCCCC1	False
6-methyl-tryptophan.params		l-ncaa/6-methyl-tryptophan.params	B40	TYPE POLYMER			True	CC1CCC2C(C[C@H](N)CO)CNC2C1	False
6-bromo-tryptophan.params		l-ncaa/6-bromo-tryptophan.params	C83	TYPE POLYMER			True	N[C@H](CO)CC1CNC2CC(Br)CCC12	False
phenyl-serine.params		l-ncaa/phenyl-serine.params	BB8	TYPE POLYMER			True	N[C@H](CO)[C@H](O)C1CCCCC1	False
7-azatryptophan.params		l-ncaa/7-azatryptophan.params	C86	TYPE POLYMER			True	N[C@H](CO)CC1CNC2NCCCC12	False
tert-butyl-cysteine.params		l-ncaa/tert-butyl-cysteine.params	C54	TYPE POLYMER			True	CC(C)(C)SC[C@H](N)CO	False
V03.params		l-ncaa/V03.params	V03	TYPE POLYMER			True	N[C@H](CO)C1CC(O)CC(O)C1	False
MPA.params	segfault					name	False		False
TES.params		l-ncaa/TES.params	TES	TYPE POLYMER			True	CC(O)N[C@H]1[C@H](O[C@@H]2[C@@H](CO)O[C@@H](NC(O)C[C@H](N)CO)[C@H](NC(C)O)[C@H]2O)O[C@H](CO)[C@@H](O[C@@H]2O[C@H](CO[C@H]3O[C@H](CO[C@H]4O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]4O)[C@@H](O)[C@H](O[C@H]4O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]4O)[C@@H]3O)[C@@H](O)[C@H](O[C@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]3O)[C@@H]2O)[C@@H]1O	False
4-fluoro-proline_puck.params		l-ncaa/4-fluoro-proline_puck.params	C89	TYPE POLYMER			True	OC[C@@H]1C[C@H](F)CN1	False
tert-butyl-alanine.params		l-ncaa/tert-butyl-alanine.params	C53	TYPE POLYMER			True	CC(C)(C)C[C@H](N)CO	False
1-methyl-histidine.params		l-ncaa/1-methyl-histidine.params	A06	TYPE POLYMER			True	CN1CNC(C[C@H](N)CO)C1	False
3-amino-tyrosine.params		l-ncaa/3-amino-tyrosine.params	A69	TYPE POLYMER	You will note that NZ1 is not protonated. This is correct! The pka of this amine is around 4.8. Wong, Shen S. Chemistry of Protein Conjugation and Cross-Linking. CRC Press, 1991.		True	NC1CC(C[C@H](N)CO)CCC1O	False
HTY.params	segfault					name	False		False
4-amino-tetrahydropyran-4-carboxylic_acid.params		l-ncaa/4-amino-tetrahydropyran-4-carboxylic_acid.params	B02	TYPE POLYMER	true NU 6 is across the CUT_BOND ICOOR_INTERNAL VCB1 59.141809 67.349267 1.528583 CA N LOWER ICOOR_INTERNAL VCA 59.141809 67.349267 1.528583 CB1 CG1 OD Fake chi to trick packer		True	NC1(CO)CCOCC1	False
alpha-methyl-tryptophan.params		l-ncaa/alpha-methyl-tryptophan.params	B60	TYPE POLYMER			True	C[C@@](N)(CO)CC1CNC2CCCCC12	False
HPR.params		l-ncaa/HPR.params	HPR	TYPE POLYMER	HPR that should work made by Ben Stranges		True	OC[C@@H]1C[C@@H](O)CN1	False
4-methyl-tryptophan.params		l-ncaa/4-methyl-tryptophan.params	B28	TYPE POLYMER	Made by Doug Renfrew		True	CC1CCCC2NCC(C[C@H](N)CO)C12	False
trifluoro-alanine.params		l-ncaa/trifluoro-alanine.params	C60	TYPE POLYMER			True	N[C@H](CO)C(F)(F)F	False
beta-cyclopentyl-alanine.params		l-ncaa/beta-cyclopentyl-alanine.params	C01	TYPE POLYMER	virt virt true NU 5 is across the CUT_BOND LOWEST_RING_CONFORMER 4C1		True	N[C@H](CO)CC1CCCC1	False
2.4-dimethyl-phenylalanine.params		l-ncaa/2.4-dimethyl-phenylalanine.params	A12	TYPE POLYMER	2,4-dimethyl-phenylalanine params file by Doug Renfrew. Tweaked by Vikram K. Mulligan (vmullig@uw.edu) on 12 March 2018.		True	CC1CCC(C[C@H](N)CO)C(C)C1	False
1-methyl-histidine_prot.params		l-ncaa/1-methyl-histidine_prot.params	A07	TYPE POLYMER			True	CN1CNC(C[C@H](N)CO)C1	False
allo-isoleucine.params		l-ncaa/allo-isoleucine.params	B47	TYPE POLYMER			True	CC[C@@H](C)[C@H](N)CO	False
MTP.params		l-ncaa/MTP.params	MTP	TYPE POLYMER	Made by Ben Stranges		True	CC1CCCC2C(C[C@H](N)CO)CNC12	False
3-aminomethyl-phenylalanine.params		l-ncaa/3-aminomethyl-phenylalanine.params	A68	TYPE POLYMER	3-aminomethyl-phenylalanine params file by Doug Renfrew. Tweaked 12 March 2018 by Vikram K. Mulligan (vmullig@uw.edu).		True	N[C@H](CO)CC1CCCC(C[NH3+])C1	False
V01.params		l-ncaa/V01.params	V01	TYPE POLYMER			True	N[C@H](CO)[C@@H](O)C1CCC(O)C(Cl)C1	False
cyclohexyl-glycine.params		l-ncaa/cyclohexyl-glycine.params	C12	TYPE POLYMER	to CB; required for ring flipping to CG1; required for ring flipping NU 6 is across the CUT_BOND …because CA is equatorial. O here is equivalent to position 6, which is CG1. must build from end of ring, unlike CB build as branch from mc, unlike CG1		True	N[C@H](CO)C1CCCCC1	False
3-methyl-phenylalanine.params		l-ncaa/3-methyl-phenylalanine.params	A84	TYPE POLYMER			True	CC1CCCC(C[C@H](N)CO)C1	False
allo-threonine.params		l-ncaa/allo-threonine.params	B48	TYPE POLYMER			True	C[C@H](O)[C@H](N)CO	False
trifluoro-leucine.params		l-ncaa/trifluoro-leucine.params	C61	TYPE POLYMER			True	C[C@H](C[C@H](N)CO)C(F)(F)F	False
BCS.params		l-ncaa/BCS.params	BCS	TYPE POLYMER			True	N[C@H](CO)CSCC1CCCCC1	False
3-hydroxy-phenylalanine.params		l-ncaa/3-hydroxy-phenylalanine.params	A78	TYPE POLYMER			True	N[C@H](CO)CC1CCCC(O)C1	False
3-chloro-phenylalanine.params		l-ncaa/3-chloro-phenylalanine.params	C95	TYPE POLYMER	kdrew: add chloro, parameters taken from 5-chloro-trp NCAA_SEMIROTAMERIC NRCHI_START_ANGLE -30		True	N[C@H](CO)CC1CCCC(Cl)C1	False
4.5-dehydro-leucine.params		l-ncaa/4.5-dehydro-leucine.params	A91	TYPE POLYMER	4,5-dehydroleucine. Params file by Doug Renfrew. Tweaked 12 March 2018 by Vikram K. Mulligan (vmullig@uw.edu).		True	CC(C)C[C@H](N)CO	False
alpha-aminoadipic_acid.params		l-ncaa/alpha-aminoadipic_acid.params	B49	TYPE POLYMER			True	N[C@H](CO)CCCC(O)O	False
7-bromo-tryptophan.params	segfault					name	False		False
amino-ethyl-cysteine.params		l-ncaa/amino-ethyl-cysteine.params	B63	TYPE POLYMER			True	N[C@H](CO)CSCC[NH3+]	False
4-fluoro-proline.params		l-ncaa/4-fluoro-proline.params	B19	TYPE POLYMER	following PRO convention true NU 5 is across the CUT_BOND LOWEST_RING_CONFORMER 4C1 ICOOR_INTERNAL NV 59.141809 67.349267 1.528583 CD2 CG CB ICOOR_INTERNAL VCD2 59.141809 67.349267 1.528583 N CA C		True	OC[C@@H]1C[C@@H](F)CN1	False
beta-fluoro-alanine.params		l-ncaa/beta-fluoro-alanine.params	C03	TYPE POLYMER			True	N[C@H](CO)CF	False
fluoro-leucine_ent1.params		l-ncaa/fluoro-leucine_ent1.params	C91	TYPE POLYMER			True	C[C@H](CF)C[C@H](N)CO	False
4-aminomethyl-phenylalanine.params		l-ncaa/4-aminomethyl-phenylalanine.params	A94	TYPE POLYMER	3-aminomethyl-phenylalanine params file by Doug Renfrew. Tweaked 12 March 2018 by Vikram K. Mulligan (vmullig@uw.edu).		True	N[C@H](CO)CC1CCC(C[NH3+])CC1	False
ornithine.params		l-ncaa/ornithine.params	ORN	TYPE POLYMER	Rosetta topology file for ornithine, commonly called “stubby lysine”. File updated 6 March 2017 by Vikram K. Mulligan (vmullig@uw.edu). Probably added by Doug Renfrew originally. residue type APL CB to side chain heavyatom distance – max observed in residue 74 of ubiquitin; taken from lysine ROTAMER_AA LYS		True	OC[C@@H]1CCC[NH2+][NH2+]1	False
5-methyl-tryptophan.params		l-ncaa/5-methyl-tryptophan.params	B38	TYPE POLYMER			True	CC1CCC2NCC(C[C@H](N)CO)C2C1	False
5-chloro-tryptophan.params	ERROR: add_bond: atom CZ2 and/or CLT don’t exist!	l-ncaa/5-chloro-tryptophan.params	C81	TYPE POLYMER			True		False
HP2.params		l-ncaa/HP2.params	HP2	TYPE POLYMER	NE2-substituted phospho-HIS is known but not reported in the PDB, so use this three letter code for now. residue type APL CB to sidechain heavy atom disance – max observed on residue 74 of ubiquitin		True	N[C@H](CO)C[C@@H]1CN([PH](O)(O)O)CN1	False
4-phenyl-phenylalanine.params		l-ncaa/4-phenyl-phenylalanine.params	B30	TYPE POLYMER	4-phenyl-phenylalanine params file created by Doug Renfrew. Tweaked 12 March 2018 by Vikram K. Mulligan (vmullig@uw.edu)		True	N[C@H](CO)CC1CCC(C2CCCCC2)CC1	False
4-hydroxy-phenylglycine.params		l-ncaa/4-hydroxy-phenylglycine.params	B21	TYPE POLYMER			True	N[C@H](CO)C1CCC(O)CC1	False
2.3-diaminopropionic_acid.params		l-ncaa/2.3-diaminopropionic_acid.params	DPP	TYPE POLYMER	2,3-diaminopropionic acid (DAP). Added a long time ago, possibly by Doug Renfrew. Updated 7 March 2017 by Vikram K. Mulligan (vmullig@uw.edu). Sadly, the PDB code for DAP is DPP, which is slightly harder to remember than DAP.		True	N[C@@H](C[NH3+])CO	False
2-indanyl-glycine_puck1.params		l-ncaa/2-indanyl-glycine_puck1.params	IGL	TYPE POLYMER			True	N[C@H](CO)C1CC2CCCCC2C1	False
beta-iodo-alanine.params		l-ncaa/beta-iodo-alanine.params	C05	TYPE POLYMER			True	N[C@H](CO)CI	False
1-amino-cyclopentane-carboxylic_acid.params	ERROR: add_bond: atom CG2 and/or CG don’t exist!	l-ncaa/1-amino-cyclopentane-carboxylic_acid.params	A04	TYPE POLYMER	true NU 5 is across the CUT_BOND ICOOR_INTERNAL VCA -16.967579 75.092865 1.530199 CB1 CG1 CG2 ICOOR_INTERNAL VCB1 -16.967579 75.092865 1.530199 CA N LOWER Fake chi to trick packer		True		False
4.5-dehydro-lysine.params		l-ncaa/4.5-dehydro-lysine.params	A92	TYPE POLYMER			True	N[C@H](CO)CCCC[NH3+]	False
2-methyl-phenylalanine.params		l-ncaa/2-methyl-phenylalanine.params	A48	TYPE POLYMER			True	CC1CCCCC1C[C@H](N)CO	False
SAL.params		l-ncaa/SAL.params	SAL	TYPE POLYMER	ICOOR_INTERNAL H -175.737237 66.220020 0.997798 N LOWER CB2		True	COC1CCC(N)CC1CO	False
beta-(1-naphthyl)-alanine.params		l-ncaa/beta-(1-naphthyl)-alanine.params	B67	TYPE POLYMER	Beta-(1-naphthyl)-alanine params file by Doug Renfrew. Tweaked 12 March 2018 by Vikram K. Mulligan (vmullig@uw.edu).		True	N[C@H](CO)CC1CCCC2CCCCC21	False
phenylglycine.params		l-ncaa/phenylglycine.params	C42	TYPE POLYMER			True	N[C@H](CO)C1CCCCC1	False
4-tert-butyl-phenylalanine.params		l-ncaa/4-tert-butyl-phenylalanine.params	B31	TYPE POLYMER			True	CC(C)(C)C1CCC(C[C@H](N)CO)CC1	False
APA.params		l-ncaa/APA.params	APA	TYPE POLYMER	Made by Douglas Renfrew (renfrew@unc.edu) and P Ben Stranges (stranges@unc.edu)		True	NC1CCC(C[C@H](N)CO)CC1	False
6-fluoro-tryptophan.params		l-ncaa/6-fluoro-tryptophan.params	C85	TYPE POLYMER			True	N[C@H](CO)CC1CNC2CC(F)CCC12	False
4-carboxy-phenylalanine.params		l-ncaa/4-carboxy-phenylalanine.params	B12	TYPE POLYMER			True	N[C@H](CO)CC1CCC(C(O)O)CC1	False
BZP.params		l-ncaa/BZP.params	BZP	TYPE POLYMER			True	N[C@H](CO)CC1CCC(C(O)C2CCCCC2)CC1	False
n-in-methyl-tryptophan.params		l-ncaa/n-in-methyl-tryptophan.params	C36	TYPE POLYMER			True	CN1CC(C[C@H](N)CO)C2CCCCC21	False
dipropyl-glycine.params		l-ncaa/dipropyl-glycine.params	C16	TYPE POLYMER			True	CCCC(N)(CO)CCC	False
LMA.params		cyclosporin/LMA.params	LMA	TYPE POLYMER	Params file for L-betamethyl-alanine (alanine with an extra methyl group on its side-chain CB). Also known as alpha-aminobutyric acid (ABA). Added 6 December 2016 by Tim Craven and Vikram K. Mulligan. residue type APL O to CB distance; max observed in ubiquitin		True	CC[C@H](N)CO	False
BMT.params	ERROR: add_bond: atom CD1 and/or CG don’t exist!	cyclosporin/BMT.params	BMT	TYPE POLYMER	Params file for (4R)-4-[(E)-2-butenyl]-4-methyl-L-threonine (BMT), a non-canonical amino acid found in cyclosporin A. Added by Tim Craven and Vikram K. Mulligan on 6 December 2016. residue type BOND CG2 2HG2 BOND CG2 3HG2 APL O to CB distance; max observed in ubiquitin		True		False