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merged.rtp
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merged.rtp
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; Peptoid versions of the canonical amino acids
[ ALAp ] ; peptoid version of alanine (sarcosine)
[ atoms ]
NL NH1 -0.210 0
CB CT3 -0.270 1
HB1 HA3 0.090 2
HB2 HA3 0.090 3
HB3 HA3 0.090 4
CA CT2 0.030 5
HA1 HB2 0.090 6
HA2 HB2 0.090 7
CLP TC 0.510 8
OL O -0.510 9
[ bonds ]
-CLP NL
NL CB
CB HB1
CB HB2
CB HB3
NL CA
CA HA1
CA HA2
CA CLP
CLP OL
CLP +NL
[ impropers ]
NL -CLP CA CB
CLP CA +NL OL
[ ARGp ] ; peptoid residue original arginine
[ atoms ]
NL NH1 -0.210 0
CB CT2 -0.180 1
HB1 HA2 0.090 2
HB2 HA2 0.090 3
CG CT2 -0.180 4
HG1 HA2 0.090 5
HG2 HA2 0.090 6
CD CT2 0.200 7
HD1 HA2 0.090 8
HD2 HA2 0.090 9
NE NC2 -0.700 10
HE HC 0.440 11
CZ C 0.640 12
NH1 NC2 -0.800 13
HH11 HC 0.460 14
HH12 HC 0.460 15
NH2 NC2 -0.800 16
HH21 HC 0.460 17
HH22 HC 0.460 18
CA CT2 0.030 19
HA1 HB2 0.090 20
HA2 HB2 0.090 21
CLP TC 0.510 22
OL O -0.510 23
[ bonds ]
-CLP NL
NL CB
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG CD
CD HD1
CD HD2
CD NE
NE HE
NE CZ
CZ NH1
CZ NH2
NH1 HH11
NH1 HH12
NH2 HH21
NH2 HH22
NL CA
CA HA1
CA HA2
CA CLP
CLP OL
CLP +NL
[ impropers ]
NL -CLP CA CB
CLP CA +NL OL
CZ NH1 NH2 NE
NH1 HH11 HH12 CZ
NH2 HH21 HH22 CZ
[ ASNp ] ; peptoid residue original aspargine
[ atoms ]
NL NH1 -0.210 0
CA CT2 0.030 1
HA1 HB2 0.090 2
HA2 HB2 0.090 3
CB CT2 -0.180 4
HB1 HA2 0.090 5
HB2 HA2 0.090 6
CG CC 0.550 7
OD1 O -0.550 8
ND2 NH2 -0.620 9
HD21 H 0.320 10
HD22 H 0.300 11
CLP TC 0.510 12
OL O -0.510 13
[ bonds ]
CB NL
CG CB
ND2 CG
NL CA
CLP CA
CLP +NL
-CLP NL
CA HA1
CA HA2
CB HB1
CB HB2
ND2 HD21
ND2 HD22
CLP OL
CG OD1
[ impropers ]
NL -CLP CA CB
CLP +NL CA OL
CG ND2 CB OD1
CG CB ND2 OD1
ND2 CG HD21 HD22
ND2 CG HD22 HD21
[ ASPd ] ; peptoid residue original ASP, used "d" instead of "p" to avoid confusion with protonated ASP
[ atoms ]
NL NH1 -0.210 0
CB CT2 -0.280 1 ; changed from CT2A (refit chi-1 params) to CT2 due to shift to peptoid
HB1 HA2 0.090 2
HB2 HA2 0.090 3
CG CC 0.620 4
OD1 OC -0.760 5
OD2 OC -0.760 6
CA CT2 0.030 7
HA1 HB2 0.090 8
HA2 HB2 0.090 9
CLP TC 0.510 10
OL O -0.510 11
[ bonds ]
-CLP NL
NL CB
CB HB1
CB HB2
CB CG
CG OD1
CG OD2
NL CA
CA HA1
CA HA2
CA CLP
CLP OL
CLP +NL
[ impropers ]
NL -CLP CA CB
CLP CA +NL OL
CG CB OD2 OD1
[ CYSd ] ; peptoid residue original cysteine
[ atoms ]
NL NH1 -0.210 0
CA CT2 0.030 1
HA1 HB2 0.090 2
HA2 HB2 0.090 3
CB CT2 -0.110 4
HB1 HA2 0.090 5
HB2 HA2 0.090 6
SG S -0.230 7
HG1 HS 0.160 9
CLP TC 0.510 10
OL O -0.510 11
[ bonds ]
-CLP NL
SG CB
NL CA
NL CB
CLP CA
CA HA1
CA HA2
CB HB1
CB HB2
SG HG1
OL CLP
CLP +NL
[ impropers ]
NL -CLP CA CB
CLP +NL CA OL
[ GLNp ] ; peptoid residue original glutamine
[ atoms ]
NL NH1 -0.210 0
CA CT2 0.030 1
HA1 HB2 0.090 2
HA2 HB2 0.090 3
CB CT2 -0.180 4
HB1 HA2 0.090 5
HB2 HA2 0.090 6
CG CT2 -0.180 7
HG1 HA2 0.090 8
HG2 HA2 0.090 9
CD CC 0.550 10
OE1 O -0.550 11
NE2 NH2 -0.620 12
HE21 H 0.320 13
HE22 H 0.300 14
CLP TC 0.510 15
OL O -0.510 16
[ bonds ]
-CLP NL
CG CB
CD CG
NE2 CD
NL CA
NL CB
CLP CA
CLP +NL
CA HA1
CA HA2
CB HB1
CB HB2
CG HG1
CG HG2
NE2 HE21
NE2 HE22
OL CLP
CD OE1
[ impropers ]
NL -CLP CA CB
CLP +NL CA OL
CD NE2 CG OE1
CD CG NE2 OE1
NE2 CD HE21 HE22
NE2 CD HE22 HE21
[ GLUd ] ; peptoid residue original GLU
[ atoms ]
NL NH1 -0.210 0
CB CT2 -0.180 1 ; changed from CT2A to CT2 due to peptoid backbone changing chi-1
HB1 HA2 0.090 2
HB2 HA2 0.090 3
CG CT2 -0.280 4
HG1 HA2 0.090 5
HG2 HA2 0.090 6
CD CC 0.620 7
OE1 OC -0.760 8
OE2 OC -0.760 9
CA CT2 0.030 10
HA1 HB2 0.090 11
HA2 HB2 0.090 12
CLP TC 0.510 13
OL O -0.510 14
[ bonds ]
-CLP NL
NL CB
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG CD
CD OE1
CD OE2
NL CA
CA HA1
CA HA2
CA CLP
CLP OL
CLP +NL
[ impropers ]
NL -CLP CA CB
CLP CA +NL OL
CD CG OE2 OE1
[ GLYp ] ; peptoid residue original glycine
[ atoms ]
NL NH1 -0.470 0
HN H 0.310 1
CA CT2 -0.020 2
HA1 HB2 0.090 3
HA2 HB2 0.090 4
CLP TC 0.510 5
OL O -0.510 6
[ bonds ]
NL HN
NL CA
CLP CA
CLP +NL
CA HA1
CA HA2
OL CLP
[ impropers ]
NL -CLP CA HN
CLP CA +NL OL
[ HSDp ] ; peptoid residue original histidine (delta-N protonated)
[ atoms ]
NL NH1 -0.210 0
CA CT2 0.030 1
HA1 HB2 0.090 2
HA2 HB2 0.090 3
CB CT2 -0.090 4
HB1 HA2 0.090 5
HB2 HA2 0.090 6
ND1 NR1 -0.360 7
HD1 H 0.320 8
CG CPH1 -0.050 9
CE1 CPH2 0.250 10
HE1 HR1 0.130 11
NE2 NR2 -0.700 12
CD2 CPH1 0.220 13
HD2 HR3 0.100 14
CLP TC 0.510 15
OL O -0.510 16
[ bonds ]
CB NL
CG CB
ND1 CG
CE1 ND1
NE2 CD2
NL CA
CLP CA
CLP +NL
-CLP NL
CA HA1
CA HA2
CB HB1
CB HB2
ND1 HD1
CD2 HD2
CE1 HE1
OL CLP
CG CD2
CE1 NE2
[ impropers ]
ND1 CG CE1 HD1
CD2 CG NE2 HD2
CE1 ND1 NE2 HE1
ND1 CE1 CG HD1
CD2 NE2 CG HD2
CE1 NE2 ND1 HE1
NL -CLP CA CB
CLP +NL CA OL
[ HSEp ] ; peptoid residue original histidine (epsilon-N protonated)
[ atoms ]
NL NH1 -0.210 0
CA CT2 0.030 1
HA1 HB2 0.090 2
HA2 HB2 0.090 3
CB CT2 -0.090 4
HB1 HA2 0.090 5
HB2 HA2 0.090 6
ND1 NR2 -0.700 7
CG CPH1 0.220 8
CE1 CPH2 0.250 9
HE1 HR1 0.130 10
NE2 NR1 -0.360 11
HE2 H 0.320 12
CD2 CPH1 -0.050 13
HD2 HR3 0.090 14
CLP TC 0.510 15
OL O -0.510 16
[ bonds ]
CB NL
CG CB
ND1 CG
NE2 CD2
NL CA
CLP CA
CLP +NL
-CLP NL
NE2 CE1
CA HA1
CA HA2
CB HB1
CB HB2
NE2 HE2
CD2 HD2
CE1 HE1
OL CLP
CD2 CG
CE1 ND1
[ impropers ]
NE2 CD2 CE1 HE2
CD2 CG NE2 HD2
CE1 ND1 NE2 HE1
NE2 CE1 CD2 HE2
CD2 NE2 CG HD2
CE1 NE2 ND1 HE1
NL -CLP CA CB
CLP +NL CA OL
[ HSPp ] ; peptoid residue original histidine (both nitrogens protonated)
[ atoms ]
NL NH1 -0.210 0
CA CT2 0.030 1
HA1 HB2 0.090 2
HA2 HB2 0.090 3
CB CT2 -0.090 4
HB1 HA2 0.090 5
HB2 HA2 0.090 6
CD2 CPH1 0.190 7
HD2 HR1 0.130 8
CG CPH1 0.190 9
NE2 NR3 -0.510 10
HE2 H 0.440 11
ND1 NR3 -0.510 12
HD1 H 0.440 13
CE1 CPH2 0.320 14
HE1 HR2 0.180 15
CLP TC 0.510 16
OL O -0.510 17
[ bonds ]
CB NL
CG CB
ND1 CG
CE1 ND1
NE2 CD2
NL CA
CLP CA
CLP +NL
-CLP NL
CA HA1
CA HA2
CB HB1
CB HB2
ND1 HD1
NE2 HE2
CD2 HD2
CE1 HE1
OL CLP
CD2 CG
NE2 CE1
[ impropers ]
ND1 CG CE1 HD1
ND1 CE1 CG HD1
NE2 CD2 CE1 HE2
NE2 CE1 CD2 HE2
NL -CLP CA CB
CLP +NL CA OL
[ ILEp ] ; peptoid residue original isoleucine
[ atoms ]
NL NH1 -0.210 0
CB CT1 -0.090 1
HB HA1 0.090 2
CG2 CT3 -0.270 3
HG21 HA3 0.090 4
HG22 HA3 0.090 5
HG23 HA3 0.090 6
CG1 CT2 -0.180 7
HG11 HA2 0.090 8
HG12 HA2 0.090 9
CD CT3 -0.270 10
HD1 HA3 0.090 11
HD2 HA3 0.090 12
HD3 HA3 0.090 13
CA CT2 0.030 14
HA1 HB2 0.090 15
HA2 HB2 0.090 16
CLP TC 0.510 17
OL O -0.510 18
[ bonds ]
-CLP NL
NL CB
CB HB
CB CG2
CG2 HG21
CG2 HG22
CG2 HG23
CB CG1
CG1 HG11
CG1 HG12
CG1 CD
CD HD1
CD HD2
CD HD3
NL CA
CA HA1
CA HA2
CA CLP
CLP OL
CLP +NL
[ impropers ]
NL -CLP CA CB
CLP CA +NL OL
[ LEUp ] ; peptoid residue original leucine
[ atoms ]
NL NH1 -0.210 0
CB CT2 -0.180 1
HB1 HA2 0.090 2
HB2 HA2 0.090 3
CG CT1 -0.090 4
HG HA1 0.090 5
CD1 CT3 -0.270 6
HD11 HA3 0.090 7
HD12 HA3 0.090 8
HD13 HA3 0.090 9
CD2 CT3 -0.270 10
HD21 HA3 0.090 11
HD22 HA3 0.090 12
HD23 HA3 0.090 13
CA CT2 0.030 14
HA1 HB2 0.090 15
HA2 HB2 0.090 16
CLP TC 0.510 17
OL O -0.510 18
[ bonds ]
-CLP NL
NL CB
CB HB1
CB HB2
CB CG
CG HG
CG CD1
CG CD2
CD1 HD11
CD1 HD12
CD1 HD13
CD2 HD21
CD2 HD22
CD2 HD23
NL CA
CA HA1
CA HA2
CA CLP
CLP OL
CLP +NL
[ impropers ]
NL -CLP CA CB
CLP CA +NL OL
[ LYSp ] ; peptoid version of lysine
[ atoms ]
NL NH1 -0.210 0
CB CT2 -0.180 1
HB1 HA2 0.090 2
HB2 HA2 0.090 3
CG CT2 -0.180 4
HG1 HA2 0.090 5
HG2 HA2 0.090 6
CD CT2 -0.180 7
HD1 HA2 0.090 8
HD2 HA2 0.090 9
CE CT2 0.210 10
HE1 HA2 0.050 11
HE2 HA2 0.050 12
NZ NH3 -0.300 13
HZ1 HC 0.330 14
HZ2 HC 0.330 15
HZ3 HC 0.330 16
CA CT2 0.030 17
HA1 HB2 0.090 18
HA2 HB2 0.090 19
CLP TC 0.510 20
OL O -0.510 21
[ bonds ]
-CLP NL
NL CB
CB HB1
CB HB2
CB CG
CG HG1
CG HG2
CG CD
CD HD1
CD HD2
CD CE
CE HE1
CE HE2
CE NZ
NZ HZ1
NZ HZ2
NZ HZ3
NL CA
CA HA1
CA HA2
CA CLP
CLP OL
CLP +NL
[ impropers ]
NL -CLP CA CB
CLP +NL CA OL
[ METd ] ; peptoid residue original methionine
[ atoms ]
NL NH1 -0.210 0
CA CT2 0.030 1
HA1 HB2 0.090 2
HA2 HB2 0.090 3
CB CT2 -0.180 4
HB1 HA2 0.090 5
HB2 HA2 0.090 6
CG CT2 -0.140 7
HG1 HA2 0.090 8
HG2 HA2 0.090 9
SD S -0.090 10
CE CT3 -0.220 11
HE1 HA3 0.090 12
HE2 HA3 0.090 13
HE3 HA3 0.090 14
CLP TC 0.510 15
OL O -0.510 16
[ bonds ]
CG CB
SD CG
CE SD
NL CB
CLP CA
NL CA
CLP +NL
NL -CLP
CA HA1
CA HA2
CB HB1
CB HB2
CG HG1
CG HG2
CE HE1
CE HE2
CE HE3
OL CLP
[ impropers ]
NL -CLP CA CB
CLP +NL CA OL
[ PHEp ] ; peptoid residue original PHE
[ atoms ]
NL NH1 -0.210 0
CB CT2 -0.180 1
HB1 HA2 0.090 2
HB2 HA2 0.090 3
CG CA 0.000 4
CD1 CA -0.115 5
HD1 HP 0.115 6
CE1 CA -0.115 7
HE1 HP 0.115 8
CZ CA -0.115 9
HZ HP 0.115 10
CD2 CA -0.115 11
HD2 HP 0.115 12
CE2 CA -0.115 13
HE2 HP 0.115 14
CA CT2 0.030 15
HA1 HB2 0.090 16
HA2 HB2 0.090 17
CLP TC 0.510 18
OL O -0.510 19
[ bonds ]
-CLP NL
NL CB
CB HB1
CB HB2
CB CG
CG CD1
CD1 CE1
CE1 CZ
CG CD2
CD2 CE2
CE2 CZ
CD1 HD1
CE1 HE1
CZ HZ
CD2 HD2
CE2 HE2
NL CA
CA HA1
CA HA2
CA CLP
CLP OL
CLP +NL
[ impropers ]
NL -CLP CA CB
CLP CA +NL OL
[ PROd ] ; peptoid residue original proline
[ atoms ]
NL NH1 -0.290 0
CD CP3 0.000 1
HD1 HA2 0.090 2
HD2 HA2 0.090 3
CA CP1 0.020 4
HA HB1 0.090 5
CB CP2 -0.180 6
HB1 HA2 0.090 7
HB2 HA2 0.090 8
CG CP2 -0.180 9
HG1 HA2 0.090 10
HG2 HA2 0.090 11
CLP TC 0.510 12
OL O -0.510 13
[ bonds ]
CLP CA
CLP +NL
NL CA
CA CB
CB CG
CG CD
NL CD
HA CA
HG1 CG
HG2 CG
HD1 CD
HD2 CD
HB1 CB
HB2 CB
OL CLP
[ impropers ]
NL -CLP CA CD
CLP CA +NL OL
[ SERp ] ; peptoid residue original serine
[ atoms ]
NL NH1 -0.210 0
CB CT2 0.050 1
HB1 HA2 0.090 2
HB2 HA2 0.090 3
OG OH1 -0.660 4
HG1 H 0.430 5
CA CT2 0.030 6
HA1 HB2 0.090 7
HA2 HB2 0.090 8
CLP TC 0.510 9
OL O -0.510 10
[ bonds ]
-CLP NL
NL CB
CB HB1
CB HB2
CB OG
OG HG1
NL CA
CA HA1
CA HA2
CA CLP
CLP OL
CLP +NL
[ impropers ]
NL -CLP CA CB
CLP CA +NL OL
[ THRp ] ; peptoid residue original threonine
[ atoms ]
NL NH1 -0.210 0
CA CT2 0.030 1
HA1 HB2 0.090 2
HA2 HB2 0.090 3
CB CT1 0.140 4
HB HA1 0.090 5
OG1 OH1 -0.660 6
HG1 H 0.430 7
CG2 CT3 -0.270 8
HG21 HA3 0.090 9
HG22 HA3 0.090 10
HG23 HA3 0.090 11
CLP TC 0.510 12
OL O -0.510 13
[ bonds ]
CB NL
OG1 CB
CG2 CB
NL CA
CLP CA
CLP +NL
CA HA1
CA HA2
CB HB
OG1 HG1
CG2 HG21
CG2 HG22
CG2 HG23
OL CLP
NL -CLP
[ impropers ]
NL -CLP CA CB
CLP +NL CA OL
[ TRPp ] ; peptoid residue original tryptophan
[ atoms ]
NL NH1 -0.210 0
CA CT2 0.030 1
HA1 HB2 0.090 2
HA2 HB2 0.090 3
CB CT2 -0.180 4
HB1 HA2 0.090 5
HB2 HA2 0.090 6
CG CY -0.030 7
CD1 CA -0.150 8
HD1 HP 0.220 9
NE1 NY -0.510 10
HE1 H 0.370 11
CE2 CPT 0.240 12
CD2 CPT 0.110 13
CE3 CAI -0.250 14
HE3 HP 0.170 15
CZ3 CA -0.200 16
HZ3 HP 0.140 17
CZ2 CAI -0.270 18
HZ2 HP 0.160 19
CH2 CA -0.140 20
HH2 HP 0.140 21
CLP TC 0.510 22
OL O -0.510 23
[ bonds ]
CG CB
CD2 CG
NE1 CD1
CZ2 CE2
NL CA
NL CB
CLP CA
CLP +NL
NL -CLP
CZ3 CH2
CD2 CE3
NE1 CE2
CA HA1
CA HA2
CB HB1
CB HB2
CD1 HD1
NE1 HE1
CE3 HE3
CZ2 HZ2
CZ3 HZ3
CH2 HH2
OL CLP
CD1 CG
CE2 CD2
CZ3 CE3
CH2 CZ2
[ impropers ]
NL -CLP CA CB
CLP +NL CA OL
[ TYRp ] ; peptoid residue original tyrosine
[ atoms ]
NL NH1 -0.210 0
CB CT2 -0.180 1
HB1 HA2 0.090 2
HB2 HA2 0.090 3
CG CA 0.000 4
CD1 CA -0.115 5
HD1 HP 0.115 6
CE1 CA -0.115 7
HE1 HP 0.115 8
CZ CA 0.110 9
OH OH1 -0.540 10
HH H 0.430 11
CD2 CA -0.115 12
HD2 HP 0.115 13
CE2 CA -0.115 14
HE2 HP 0.115 15
CA CT2 0.030 16
HA1 HB2 0.090 17
HA2 HB2 0.090 18
CLP TC 0.510 19
OL O -0.510 20
[ bonds ]
-CLP NL
NL CB
CB HB1
CB HB2
CB CG
CG CD1
CG CD2
CD1 CE1
CD2 CE2
CE1 CZ
CE2 CZ
CD1 HD1
CD2 HD2
CE1 HE1
CE2 HE2
CZ OH
OH HH
NL CA
CA HA1
CA HA2
CA CLP
CLP OL
CLP +NL
[ impropers ]
NL -CLP CA CB
CLP CA +NL OL
[ VALp ] ; peptoid residue original valine
[ atoms ]
NL NH1 -0.210 0
CA CT2 0.030 1
HA1 HB2 0.090 2
HA2 HB2 0.090 3
CB CT1 -0.090 4
HB HA1 0.090 5
CG1 CT3 -0.270 6
HG11 HA3 0.090 7
HG12 HA3 0.090 8
HG13 HA3 0.090 9
CG2 CT3 -0.270 10
HG21 HA3 0.090 11
HG22 HA3 0.090 12
HG23 HA3 0.090 13
CLP TC 0.510 14
OL O -0.510 15
[ bonds ]
CB NL
CG1 CB
CG2 CB
NL CA
NL -CLP
CLP CA
CLP +NL
CA HA1
CA HA2
CB HB
CG1 HG11
CG1 HG12
CG1 HG13
CG2 HG21
CG2 HG22
CG2 HG23
OL CLP
[ impropers ]
NL -CLP CA CB
CLP +NL CA OL
[ ACEp ] ; N-terminal acetyl patch EDITED FOR PEPTOIDS
[ atoms ]
CAY CT3 -0.270 1
HY1 HA3 0.090 1
HY2 HA3 0.090 1
HY3 HA3 0.090 1
CLP TC 0.510 2
OL O -0.510 2
[ bonds ]
CLP CAY
CLP +NL
CAY HY1
CAY HY2
CAY HY3
OL CLP
[ impropers ]
CLP CAY +NL OL
[ NMEp ] ; terminal residue, provided by Mark Abraham EDITED FOR PEPTOIDS
; renamed by Justin Lemkul to avoid clash with N-methylacetamide
[ atoms ]
NL NH1 -0.470 1
HNT H 0.310 1
CAT CT3 -0.110 1
HT1 HA3 0.090 1
HT2 HA3 0.090 1
HT3 HA3 0.090 1
[ bonds ]
-CLP NL
NL HNT
NL CAT
CAT HT1
CAT HT2
CAT HT3
[ impropers ]
NL -CLP CAT HNT
-CLP CAT NL -OL
; Additional Residues requested by CLC + Co.
[ NSPE ] ;for both nrpe and nspe we can rename this one if you want!
[ atoms ]
NL NH1 -0.42 0
CB1 CT2 0.12 1
HB1 HA2 0.09 2
CB2 CT3 -0.27 3
HB2 HA3 0.09 4
HB3 HA3 0.09 5
HB4 HA3 0.09 6
CG CG2R61 0.00 7
CD1 CG2R61 -0.15 8
HD1 HGR61 0.15 9
CD2 CG2R61 -0.15 10
HD2 HGR61 0.15 11
CE1 CG2R61 -0.15 12
HE1 HGR61 0.15 13
CE2 CG2R61 -0.15 14
HE2 HGR61 0.15 15
CH CG2R61 -0.15 16
HC HGR61 0.15 17
CA CT2 0.03 18
HA1 HB2 0.09 19
HA2 HB2 0.09 20
CLP TC 0.51 21
OL O -0.51 22