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aminoacids.ff
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; Copyright 2018 University of Groningen
;
; Licensed under the Apache License, Version 2.0 (the "License");
; you may not use this file except in compliance with the License.
; You may obtain a copy of the License at
;
; http://www.apache.org/licenses/LICENSE-2.0
;
; Unless required by applicable law or agreed to in writing, software
; distributed under the License is distributed on an "AS IS" BASIS,
; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
; See the License for the specific language governing permissions and
; limitations under the License.
[ macros ]
protein_resnames "GLY|ALA|CYS|VAL|LEU|ILE|MET|PRO|HYP|ASN|GLN|ASP|ASP0|GLU|GLU0|THR|SER|LYS|LYS0|ARG|ARG0|HIS|HISH|PHE|TYR|TRP"
protein_resnames_non_pro "GLY|ALA|CYS|VAL|LEU|ILE|MET|ASN|GLN|ASP|ASP0|GLU|GLU0|THR|SER|LYS|LYS0|ARG|ARG0|HIS|HISH|PHE|TYR|TRP"
prot_default_bb_type P2
stiff_fc 1000000
[ variables ]
elastic_network_bond_type 1
res_min_dist 3
[ citations ]
Martini3
polyply
M3_GO
;;; GLYCINE
[ moleculetype ]
; molname nrexcl
GLY 1
[ atoms ]
;id type resnr residu atom cgnr charge mass
1 SP1 1 GLY BB 1 0
2 VS 1 GLY CA 1 0 0
[ position_restraints ]
1 1 1000 1000 1000 {"ifdef": "POSRES"}
[ virtual_sitesn ]
2 1 -- 1
;;; ALANINE
[ moleculetype ]
; molname nrexcl
ALA 1
[ atoms ]
;id type resnr residu atom cgnr charge
1 SP2 1 ALA BB 1 0
2 TC3 1 ALA SC1 1 0
3 VS 1 ALA CA 1 0 0
[ virtual_sitesn ]
3 1 -- 1
[ constraints ]
#meta {"group": "Side chain bonds", "ifndef": "FLEXIBLE"}
; i j funct length
BB SC1 1 0.270
[ bonds ]
#meta {"group": "Side chain bonds", "ifdef": "FLEXIBLE"}
; i j funct length
BB SC1 1 0.270 $stiff_fc
[ position_restraints ]
1 1 1000 1000 1000 {"ifdef": "POSRES"}
;;; CYSTEINE
[ moleculetype ]
; molname nrexcl
CYS 1
[ atoms ]
;id type resnr residu atom cgnr charge
1 $prot_default_bb_type 1 CYS BB 1 0
2 TC6 1 CYS SC1 1 0
3 VS 1 CYS CA 1 0 0
[ virtual_sitesn ]
3 1 -- 1
[bonds]
#meta {"group": "Side chain bonds"}
; i j funct length force.c.
BB SC1 1 0.341 7500
[ position_restraints ]
1 1 1000 1000 1000 {"ifdef": "POSRES"}
;;; VALINE
[ moleculetype ]
; molname nrexcl
VAL 1
[ atoms ]
;id type resnr residu atom cgnr charge
1 SP2 1 VAL BB 1 0
2 SC3 1 VAL SC1 1 0
3 VS 1 VAL CA 1 0 0
[ virtual_sitesn ]
3 1 -- 1
[ constraints ]
#meta {"group": "Side chain bonds", "ifndef": "FLEXIBLE"}
; i j funct length
BB SC1 1 0.292
[ bonds ]
#meta {"group": "Side chain bonds", "ifdef": "FLEXIBLE"}
; i j funct length
BB SC1 1 0.292 $stiff_fc
[ position_restraints ]
1 1 1000 1000 1000 {"ifdef": "POSRES"}
;;; LEUCINE
[ moleculetype ]
; molname nrexcl
LEU 1
[ atoms ]
;id type resnr residu atom cgnr charge
1 $prot_default_bb_type 1 LEU BB 1 0
2 SC2 1 LEU SC1 1 0
3 VS 1 LEU CA 1 0 0
[ virtual_sitesn ]
3 1 -- 1
[bonds]
#meta {"group": "Side chain bonds"}
; i j funct length force.c.
BB SC1 1 0.363 7500
[ position_restraints ]
1 1 1000 1000 1000 {"ifdef": "POSRES"}
;;; ISOLEUCINE
[ moleculetype ]
; molname nrexcl
ILE 1
[ atoms ]
;id type resnr residu atom cgnr charge
1 $prot_default_bb_type 1 ILE BB 1 0
2 SC2 1 ILE SC1 1 0
3 VS 1 ILE CA 1 0 0
[ virtual_sitesn ]
3 1 -- 1
[ constraints ]
#meta {"group": "Side chain bonds", "ifndef": "FLEXIBLE"}
; i j funct length
BB SC1 1 0.341
[ bonds ]
#meta {"group": "Side chain bonds", "ifdef": "FLEXIBLE"}
; i j funct length
BB SC1 1 0.341 $stiff_fc
[ position_restraints ]
1 1 1000 1000 1000 {"ifdef": "POSRES"}
;;; METHIONINE
[ moleculetype ]
; molname nrexcl
MET 1
[ atoms ]
;id type resnr residu atom cgnr charge
1 $prot_default_bb_type 1 MET BB 1 0
2 C6 1 MET SC1 1 0
3 VS 1 MET CA 1 0 0
[ virtual_sitesn ]
3 1 -- 1
[bonds]
#meta {"group": "Side chain bonds"}
; i j funct length force.c.
BB SC1 1 0.40 2500
[ position_restraints ]
1 1 1000 1000 1000 {"ifdef": "POSRES"}
;;; PROLINE
[ moleculetype ]
; molname nrexcl
PRO 1
[ atoms ]
;id type resnr residu atom cgnr charge
1 SP2a 1 PRO BB 1 0
2 SC3 1 PRO SC1 1 0
3 VS 1 PRO CA 1 0 0
[ virtual_sitesn ]
3 1 -- 1
[bonds]
#meta {"group": "Side chain bonds"}
; i j funct length force.c.
BB SC1 1 0.330 7500
[ position_restraints ]
1 1 1000 1000 1000 {"ifdef": "POSRES"}
[ moleculetype ]
; molname nrexcl
HYP 1
[ atoms ]
;id type resnr residu atom cgnr charge
1 P1 1 HYP BB 1 0
2 P1 1 HYP SC1 1 0
3 VS 1 HYP CA 1 0 0
[ virtual_sitesn ]
3 1 -- 1
[bonds]
#meta {"group": "Side chain bonds"}
; i j funct length force.c.
BB SC1 1 0.300 7500
[ position_restraints ]
1 1 1000 1000 1000 {"ifdef": "POSRES"}
;;; ASPARAGINE
[ moleculetype ]
; molname nrexcl
ASN 1
[ atoms ]
;id type resnr residu atom cgnr charge
1 $prot_default_bb_type 1 ASN BB 1 0
2 SP5 1 ASN SC1 1 0
3 VS 1 ASN CA 1 0 0
[ virtual_sitesn ]
3 1 -- 1
[bonds]
#meta {"group": "Side chain bonds"}
; i j funct length force.c.
BB SC1 1 0.352 5000
[ position_restraints ]
1 1 1000 1000 1000 {"ifdef": "POSRES"}
;;; GLUTAMINE
[ moleculetype ]
; molname nrexcl
GLN 1
[ atoms ]
;id type resnr residu atom cgnr charge
1 $prot_default_bb_type 1 GLN BB 1 0
2 P5 1 GLN SC1 1 0
3 VS 1 GLN CA 1 0 0
[ virtual_sitesn ]
3 1 -- 1
[bonds]
#meta {"group": "Side chain bonds"}
; i j funct length force.c.
BB SC1 1 0.400 5000
[ position_restraints ]
1 1 1000 1000 1000 {"ifdef": "POSRES"}
;;; ASPARTATE
[ moleculetype ]
; molname nrexcl
ASP 1
[ atoms ]
;id type resnr residu atom cgnr charge
1 $prot_default_bb_type 1 ASP BB 1 0
2 SQ5n 1 ASP SC1 1 -1.0
3 VS 1 ASP CA 1 0 0
[ virtual_sitesn ]
3 1 -- 1
[bonds]
#meta {"group": "Side chain bonds"}
; i j funct length force.c.
BB SC1 1 0.352 7500
[ position_restraints ]
1 1 1000 1000 1000 {"ifdef": "POSRES"}
;;; GLUTAMATE
[ moleculetype ]
; molname nrexcl
GLU 1
[ atoms ]
;id type resnr residu atom cgnr charge
1 $prot_default_bb_type 1 GLU BB 1 0
2 Q5n 1 GLU SC1 1 -1.0
3 VS 1 GLU CA 1 0 0
[ virtual_sitesn ]
3 1 -- 1
[bonds]
#meta {"group": "Side chain bonds"}
; i j funct length force.c.
BB SC1 1 0.400 5000
[ position_restraints ]
1 1 1000 1000 1000 {"ifdef": "POSRES"}
;;; THREONINE
[ moleculetype ]
; molname nrexcl
THR 1
[ atoms ]
;id type resnr residu atom cgnr charge
1 $prot_default_bb_type 1 THR BB 1 0
2 SP1 1 THR SC1 1 0
3 VS 1 THR CA 1 0 0
[ virtual_sitesn ]
3 1 -- 1
[ constraints ]
#meta {"group": "Side chain bonds", "ifndef": "FLEXIBLE"}
; i j funct length (Modified by Paulo)
BB SC1 1 0.305
[ bonds ]
#meta {"group": "Side chain bonds", "ifdef": "FLEXIBLE"}
; i j funct length
BB SC1 1 0.305 $stiff_fc
[ position_restraints ]
1 1 1000 1000 1000 {"ifdef": "POSRES"}
;;; SERINE
[ moleculetype ]
; molname nrexcl
SER 1
[ atoms ]
;id type resnr residu atom cgnr charge
1 $prot_default_bb_type 1 SER BB 1 0
2 TP1 1 SER SC1 1 0
3 VS 1 SER CA 1 0 0
[ virtual_sitesn ]
3 1 -- 1
[bonds]
#meta {"group": "Side chain bonds"}
; i j funct length force.c.
BB SC1 1 0.287 7500
[ position_restraints ]
1 1 1000 1000 1000 {"ifdef": "POSRES"}
;;; LYSINE
[ moleculetype ]
; molname nrexcl
LYS 1
[ atoms ]
;id type resnr residu atom cgnr charge
1 $prot_default_bb_type 1 LYS BB 1 0
2 SC3 1 LYS SC1 1 0
3 SQ4p 1 LYS SC2 1 1.0
4 VS 1 LYS CA 1 0 0
[ virtual_sitesn ]
4 1 -- 1
[bonds]
#meta {"group": "Side chain bonds"}
; i j funct length force.c.
BB SC1 1 0.330 5000
SC1 SC2 1 0.360 5000
[angles]
#meta {"group": "Side chain angles"}
; i j k funct angle force.c.
BB SC1 SC2 2 180.000 25.0
[ position_restraints ]
1 1 1000 1000 1000 {"ifdef": "POSRES"}
;;; ARGININE
[ moleculetype ]
; molname nrexcl
ARG 1
[ atoms ]
;id type resnr residu atom cgnr charge
1 $prot_default_bb_type 1 ARG BB 1 0
2 SC3 1 ARG SC1 1 0
3 SQ3p 1 ARG SC2 1 1.0
4 VS 1 ARG CA 1 0 0
[ virtual_sitesn ]
4 1 -- 1
[bonds]
#meta {"group": "Side chain bonds"}
; i j funct length force.c.
BB SC1 1 0.330 5000
SC1 SC2 1 0.380 5000
[angles]
#meta {"group": "Side chain angles"}
; i j k funct angle force.c.
BB SC1 SC2 2 180.000 25.0
[ position_restraints ]
1 1 1000 1000 1000 {"ifdef": "POSRES"}
;;; HISTIDINE
[ moleculetype ]
;molname nrexcl
HIS 1
[ atoms ]
;id type resnr residu atom cgnr charge
1 $prot_default_bb_type 1 HIS BB 1 0
2 TC4 1 HIS SC1 1 0 ; three side chains in triangle
3 TN6d 1 HIS SC2 1 0 ; configuration, mimicking
4 TN5a 1 HIS SC3 1 0 ; ring structure
5 VS 1 HIS CA 1 0 0
[ virtual_sitesn ]
5 1 -- 1
[ bonds ]
#meta {"group": "Side chain bonds"}
; i j funct length force.c.
BB SC1 1 0.336 7500
#meta {"group": "Side chain bonds", "ifdef": "FLEXIBLE"}
; i j funct length
SC1 SC2 1 0.320 $stiff_fc
SC1 SC3 1 0.300 $stiff_fc
SC2 SC3 1 0.270 $stiff_fc
[ constraints ]
#meta {"group": "Side chain bonds", "ifndef": "FLEXIBLE"}
; i j funct length
SC1 SC2 1 0.320
SC1 SC3 1 0.300
SC2 SC3 1 0.270
[angles]
#meta {"group": "Side chain angles"}
; i j k funct angle force.c.
BB SC1 SC2 2 120.000 50.0
BB SC1 SC3 2 120.000 50.0
;[dihedrals]
; i j k l funct angle force.c.
; BB SC2 SC3 SC1 2 0.0 50.0 ; to prevent backflipping of ring
[exclusions]
; We do not want non-bounded interactions within the residue.
BB SC1 SC2 SC3
SC1 SC2 SC3
SC2 SC3
[ position_restraints ]
1 1 1000 1000 1000 {"ifdef": "POSRES"}
[ moleculetype ]
;molname nrexcl
HIH 1
[ atoms ]
;id type resnr residu atom cgnr charge
1 $prot_default_bb_type 1 HIS BB 1 0
2 TC4 1 HIH SC1 2 0 ; three side chains in triangle
3 TN6d 1 HIH SC2 3 0 ; configuration, mimicking
4 TQ2p 1 HIH SC3 4 1 ; ring structure
;2 TC4 1 HIH SC1 2 0 ; three side chains in triangle
;3 TP3dq 1 HIH SC2 3 +0.5 ; modelB
;4 TP3dq 1 HIH SC3 4 +0.5 ;
5 VS 1 HIH CA 1 0 0
[ virtual_sitesn ]
5 1 -- 1
[bonds]
#meta {"group": "Side chain bonds"}
; i j funct length force.c.
BB SC1 1 0.336 7500
#meta {"group": "Side chain bonds", "ifdef": "FLEXIBLE"}
; i j funct length
SC1 SC2 1 0.320 $stiff_fc
SC1 SC3 1 0.300 $stiff_fc
SC2 SC3 1 0.270 $stiff_fc
[constraints]
#meta {"group": "Side chain bonds", "ifndef": "FLEXIBLE"}
; i j funct length
SC1 SC2 1 0.320
SC1 SC3 1 0.300
SC2 SC3 1 0.270
[angles]
#meta {"group": "Side chain angles"}
; i j k funct angle force.c.
BB SC1 SC2 2 120.000 50.0
BB SC1 SC3 2 120.000 50.0
;[dihedrals]
; i j k l funct angle force.c.
; BB SC2 SC3 SC1 2 0.0 50.0 ; to prevent backflipping of ring
[exclusions]
; We do not want non-bounded interactions within the residue.
BB SC1 SC2 SC3
SC1 SC2 SC3
SC2 SC3
[ position_restraints ]
1 1 1000 1000 1000 {"ifdef": "POSRES"}
;;; PHENYLALANINE
[ moleculetype ]
; molname nrexcl
PHE 1
[ atoms ]
;id type resnr residu atom cgnr charge
1 $prot_default_bb_type 1 PHE BB 1 0
2 SC4 1 PHE SC1 1 0 ; three side chains in triangle
3 TC5 1 PHE SC2 1 0 ; configuration, mimicking
4 TC5 1 PHE SC3 1 0 ; ring structure
5 VS 1 PHE CA 1 0 0
[ virtual_sitesn ]
5 1 -- 1
[bonds]
#meta {"group": "Side chain bonds"}
; i j funct length force.c.
BB SC1 1 0.325 7500
#meta {"group": "Side chain bonds", "ifdef": "FLEXIBLE"}
; i j funct length
SC1 SC2 1 0.340 $stiff_fc
SC1 SC3 1 0.340 $stiff_fc
SC2 SC3 1 0.290 $stiff_fc
[constraints]
#meta {"group": "Side chain bonds", "ifndef": "FLEXIBLE"}
; i j funct length
SC1 SC2 1 0.340
SC1 SC3 1 0.340
SC2 SC3 1 0.290
[angles]
#meta {"group": "Side chain angles"}
; i j k funct angle force.c.
BB SC1 SC2 2 120.000 50.0
BB SC1 SC3 2 120.000 50.0
;[dihedrals]
; i j k l funct angle force.c.
; BB SC2 SC3 SC1 2 0.0 50.0 ; to prevent backflipping of ring
[exclusions]
; We do not want non-bounded interactions within the residue.
BB SC1 SC2 SC3
SC1 SC2 SC3
SC2 SC3
[ position_restraints ]
1 1 1000 1000 1000 {"ifdef": "POSRES"}
;;; TYROSINE
[ moleculetype ]
; molname nrexcl
TYR 1
[ atoms ]
;id type resnr residu atom cgnr charge
1 $prot_default_bb_type 1 TYR BB 1 0
2 TC4 1 TYR SC1 1 0
3 TC5 1 TYR SC2 1 0
4 TC5 1 TYR SC3 1 0
5 TN6 1 TYR SC4 1 0
6 VS 1 TYR CA 1 0 0
[ virtual_sitesn ]
6 1 -- 1
[bonds]
#meta {"group": "Side chain bonds"}
; i j funct length force.c.
BB SC1 1 0.325 5000
#meta {"group": "Side chain bonds", "ifdef": "FLEXIBLE"}
; i j funct length
SC1 SC2 1 0.300 $stiff_fc
SC1 SC3 1 0.300 $stiff_fc
SC2 SC4 1 0.285 $stiff_fc
SC3 SC4 1 0.285 $stiff_fc
SC2 SC3 1 0.300 $stiff_fc
[constraints]
#meta {"group": "Side chain bonds", "ifndef": "FLEXIBLE"}
; i j funct length
SC1 SC2 1 0.300
SC1 SC3 1 0.300
SC2 SC4 1 0.285
SC3 SC4 1 0.285
SC2 SC3 1 0.300
[angles]
#meta {"group": "Side chain angles"}
; i j k funct angle force.c.
BB SC1 SC2 2 120.000 60.0
BB SC1 SC3 2 120.000 60.0
[dihedrals]
; i j k l funct angle force.c.
SC4 SC2 SC3 SC1 2 180.0 50.0 ; to prevent backflipping of ring
[exclusions]
; We do not want non-bounded interactions within the residue.
BB SC1 SC2 SC3 SC4
SC1 SC2 SC3 SC4
SC2 SC3 SC4
SC3 SC4
[ position_restraints ]
1 1 1000 1000 1000 {"ifdef": "POSRES"}
;;; TRYPTOPHAN
[ moleculetype ]
;molname nrexcl
TRP 1
[ atoms ]
;id type resnr residu atom cgnr charge
1 $prot_default_bb_type 1 TRP BB 1 0
2 TC4 1 TRP SC1 1 0 36
3 TN6d 1 TRP SC2 1 0 36
4 TC5 1 TRP SC3 1 0 0
5 TC5 1 TRP SC4 1 0 36
6 TC5 1 TRP SC5 1 0 36
7 VS 1 TRP CA 1 0 0
[ bonds ]
#meta {"group": "Side chain bonds"}
; i j funct length force.c.
BB SC1 1 0.315 5000
#meta {"group": "Side chain bonds", "ifdef": "FLEXIBLE"}
; i j funct length
SC1 SC2 1 0.335 $stiff_fc
SC2 SC5 1 0.412 $stiff_fc
SC4 SC5 1 0.293 $stiff_fc
SC1 SC4 1 0.404 $stiff_fc
SC2 SC4 1 0.470 $stiff_fc
[ constraints ]
#meta {"group": "Side chain bonds", "ifndef": "FLEXIBLE"}
; i j funct length
SC1 SC2 1 0.335
SC2 SC5 1 0.412
SC4 SC5 1 0.293
SC1 SC4 1 0.404
SC2 SC4 1 0.470
[ angles ]
#meta {"group": "Side chain angles"}
; i j k funct angle force.c.
BB SC1 SC2 2 120.000 60.0
BB SC1 SC4 2 130.000 60.0
[ dihedrals ]
; i j k l funct angle force.c.
SC5 SC4 SC2 SC1 2 180.0 100.0
[ virtual_sitesn ]
SC3 SC5 SC4 SC2 SC1 -- 2
7 1 -- 1
; prevents polyply warning about disconnected molecules
[ edges ]
SC3 SC5
[exclusions]
; We do not want non-bounded interactions within the residue.
BB SC1 SC2 SC3 SC4 SC5
SC1 SC2 SC3 SC4 SC5
SC2 SC3 SC4 SC5
SC3 SC4 SC5
SC4 SC5
[ position_restraints ]
1 1 1000 1000 1000 {"ifdef": "POSRES"}
;;; Links
;; Links for COIL. We apply them first as coil is the default.
[ link ]
resname $protein_resnames
[ bonds ]
; (Modified by Paulo)
BB +BB 1 0.350 4000 {"group": "Backbone bonds"}
[ link ]
resname $protein_resnames
[ angles ]
-BB BB SC1 2 100 25 {"group": "BBS angles regular martini", "version": 1}
[ link ]
resname $protein_resnames
[ angles ]
#meta {"group": "First SBB regular martini"}
SC1 BB +BB 2 100 25 {"version": 1}
[ non-edges ]
BB -BB
[ link ]
-BB { }
BB { }
+BB { }
[ angles ]
; (Modified by Paulo)
-BB BB +BB 10 127 25 {"group": "BBB angles"}
[ patterns ]
-BB BB {"resname": "PRO|HYP"} +BB
-BB {"resname": "PRO|HYP"} BB +BB
-BB BB +BB {"resname": "PRO|HYP"}
[ link ]
resname $protein_resnames
[ angles ]
; (Modified by Paulo)
-BB BB +BB 10 127 20 {"group": "BBB angles"}
[ patterns ]
-BB BB {"resname": $protein_resnames_non_pro} +BB
-BB {"resname": $protein_resnames_non_pro} BB +BB
-BB BB +BB {"resname": $protein_resnames_non_pro}
;; IDP specific corrections
[ link ]
resname $protein_resnames
[ angles ]
BB +BB +SC1 10 85 10 {"group": "idp-fix"}
[ link ]
resname $protein_resnames
[ angles ]
-SC1 -BB BB 10 85 10 {"group": "idp-fix"}
[ link ]
resname $protein_resnames
[ dihedrals ]
BB +BB ++BB +++BB 9 -120 -1 1 {"group": "idp-fix", "comment": "BB-BB-BB-BB-v1", "version":1}
BB +BB ++BB +++BB 9 -120 -1 2 {"group": "idp-fix", "comment": "BB-BB-BB-BB-v2", "version":2}
[ link ]
resname $protein_resnames
[ dihedrals ]
SC1 BB +BB +SC1 9 -130 -1.5 1 {"group": "idp-fix", "version": 1, "comment": "SC1-BB-BB-SC1-v1"}
SC1 BB +BB +SC1 9 100 -1.5 2 {"group": "idp-fix", "version": 2, "comment": "SC1-BB-BB-SC1-v2"}
[ link ]
[ atoms ]
-SC1 {"resname": $protein_resnames}
-BB {"resname": $protein_resnames}
BB {"resname": "GLY"}
+BB {"resname": $protein_resnames}
[ dihedrals ]
-SC1 -BB BB +BB 1 115 -4.5 1 {"group": "idp-fix", "comment": "SC1-BB-BB(GLY)-BB"}
[ link ]
[ atoms ]
-BB {"resname": $protein_resnames}
BB {"resname": "GLY"}
+BB {"resname": $protein_resnames}
+SC1 {"resname": $protein_resnames}
[ dihedrals ]
-BB BB +BB +SC1 1 0 -2.0 1 {"group": "idp-fix", "comment": "BB-BB(GLY)-BB-SC1"}
[ link ]
resname $protein_resnames
[ exclusions ]
#meta {"comment": "CA-BB-same"}
CA BB
[ edges ]
CA BB
[ link ]
resname $protein_resnames
[ atoms ]
CA { }
BB { }
+BB { }
[ exclusions ]
#meta {"comment": "CA-BB"}
CA +BB
[ edges ]
BB +BB
;; Protein termini. These links should be applied last.
[ link ]
resname $protein_resnames
[ atoms ]
BB {"replace": {"atype": "Q5", "charge": 1}}
[ non-edges ]
BB -BB
[ link ]
resname $protein_resnames
[ atoms ]
BB {"replace": {"atype": "Q5", "charge": -1}}
[ non-edges ]
BB +BB
[ link ]
resname $protein_resnames
[ atoms ]
BB {"replace": {"atype": "P6", "charge": 0}}
[ non-edges ]
BB +BB
BB -BB
[ link ]
resname $protein_resnames
[ molmeta ]
neutral_termini true
[ atoms ]
BB {"replace": {"atype": "P5", "charge": 0}}
[ non-edges ]
BB -BB
[ link ]
resname $protein_resnames
[ molmeta ]
neutral_termini true
[ atoms ]
BB {"replace": {"atype": "P6", "charge": 0}}
[ non-edges ]
BB +BB
;; Cystein bridge
[ link ]
resname "CYS"
[ constraints ]
SC1 >SC1 1 0.24 {"comment": "Disulfide bridge"}
[ features ]
disulfide