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martini_v3.0.0_small_molecules_v1.itp
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martini_v3.0.0_small_molecules_v1.itp
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;;;;; Martini 3 - Database of small molecules - Topologies with optimized bond lengths
;;;;;
;;;;; File updated on 2021-11-01
;;;;; Currently, there are 90 topologies.
;;;;; Version: 3.0.0_v1
;;;;;
;;;;; If you use or wish to cite the Martini 3 small-molecule database, please refer to the following publication:
;;;;; R Alessandri, et al., Adv. Theory Simul., 2022, DOI: https://doi.org/10.1002/adts.202100391
;;;;;
;;;;; Note(s):
;;;;; Additional references and/or notes relevant to a specific model may be provided in the header of
;;;;; the topology of a particular molecule.
;;;;; MONOcyclic compounds
;;;;;; 1-METHYLIMIDAZOLE
[moleculetype]
; molname nrexcl
1MIMI 1
[atoms]
; id type resnr residu atom cgnr charge
1 TN1 1 1MIMI N1 1 0
2 TN6a 1 1MIMI N2 2 0
3 TC5 1 1MIMI R3 3 0
[constraints]
; i j funct length
1 2 1 0.285
2 3 1 0.270
1 3 1 0.315
;;;;;; 2-METHYL-PYRIDINE
[moleculetype]
; molname nrexcl
2MPYR 1
[atoms]
; id type resnr residu atom cgnr charge
1 SC4 1 2MPYR R1 1 0
2 TN6a 1 2MPYR N2 2 0
3 TC5 1 2MPYR R3 3 0
[constraints]
; i j funct length
1 2 1 0.295
2 3 1 0.285
1 3 1 0.295
;;;;;; 2-NITRO-m-XYLENE
;
; Note(s):
; For minimizations, you may use define=-DFLEXIBLE to use a stiff-bond version of the topology that is more amenable to minimization.
;
[moleculetype]
; molname nrexcl
2NIMX 1
[atoms]
; id type resnr residu atom cgnr charge
1 SN3a 1 2NIMX N1 1 0
2 SC4 1 2NIMX R2 2 0
3 SC4 1 2NIMX R3 3 0
4 TC5 1 2NIMX R4 4 0
[bonds]
#ifndef FLEXIBLE
[constraints]
#endif
; i j funct length
1 2 1 0.304 1000000 ; cog
1 3 1 0.304 1000000 ; cog
2 3 1 0.450 1000000 ; cog
2 4 1 0.361 1000000 ; cog
3 4 1 0.361 1000000 ; cog
[dihedrals]
; i j k l funct ref.angle force_k
1 2 3 4 2 180.00 100
[exclusions]
1 4
;;;;;; 2-NITROTOLUENE
;
; Note(s):
; For minimizations, you may use define=-DFLEXIBLE to use a stiff-bond version of the topology that is more amenable to minimization.
;
[moleculetype]
; molname nrexcl
2NITL 1
[atoms]
; id type resnr residu atom cgnr charge
1 SN3a 1 2NITL N1 1 0
2 SC4 1 2NITL R2 2 0
3 TC5 1 2NITL R3 3 0
4 TC5 1 2NITL R4 4 0
[bonds]
#ifndef FLEXIBLE
[constraints]
#endif
; i j funct length
1 2 1 0.281 1000000 ; cog
1 3 1 0.317 1000000 ; cog
2 3 1 0.369 1000000 ; cog
2 4 1 0.281 1000000 ; cog
3 4 1 0.362 1000000 ; cog
[dihedrals]
; i j k l funct ref.angle force_k
1 2 3 4 2 180.00 100
[exclusions]
1 4
;;;;;; 3-HEXYL-THIOPHENE
;
; Reference(s):
; R Alessandri, JJ Uusitalo, AH de Vries, RWA Havenith, SJ Marrink, Bulk Heterojunction Morphologies with Atomistic Resolution
; from Coarse-Grain Solvent Evaporation Simulations, JACS 2017, 139, 3697 [DOI: 10.1021/jacs.6b11717]
;
; Note(s):
; Topology adpated from the Martini 2.2 P3HT model [DOI: 10.1021/jacs.6b11717] to Martini 3.
; THIOphene bonded parameters are from the optimized Martini 3 THIO model.
;
[moleculetype]
; molname nrexcl
3HT 1
[atoms]
; nr type resnr residue atom cgnr charge mass
1 TC6 1 3HT S1 1 0
2 TC5 1 3HT R2 2 0
3 TC5 1 3HT R3 3 0
4 SC2 1 3HT C4 4 0
5 SC2 1 3HT C5 5 0
[bonds]
; atoms funct length force_k
4 5 1 0.360 5000 ; [DOI:10.1021/jacs.6b11717]
[constraints]
; i j funct length
; thiophene
1 2 1 0.270 ; Martini 3 THIO model
1 3 1 0.270 ; Martini 3 THIO model
2 3 1 0.280 ; Martini 3 THIO model
; thiophene-hexyl
3 4 1 0.285 ; [DOI:10.1021/jacs.6b11717]
[angles]
; i j k funct angle force_k
1 3 4 2 180 250 ; [DOI:10.1021/jacs.6b11717]
3 4 5 1 155 25 ; [DOI:10.1021/jacs.6b11717]
;;;;;; 3-PROPYL-THIOPHENE
;
; Reference(s):
; R Alessandri, JJ Uusitalo, AH de Vries, RWA Havenith, SJ Marrink, Bulk Heterojunction Morphologies with Atomistic Resolution
; from Coarse-Grain Solvent Evaporation Simulations, JACS 2017, 139, 3697 [DOI: 10.1021/jacs.6b11717]
;
; Note(s):
; Topology adpated from the Martini 2.2 P3HT model [DOI: 10.1021/jacs.6b11717] to Martini 3.
; THIOphene bonded parameters are from the optimized Martini 3 THIO model.
;
[moleculetype]
; molname nrexcl
3PT 1
[atoms]
; nr type resnr residue atom cgnr charge mass
1 TC6 1 3PT S1 1 0
2 TC5 1 3PT R2 2 0
3 TC5 1 3PT R3 3 0
4 SC2 1 3PT C4 4 0
[constraints]
; i j funct length
; thiophene
1 2 1 0.270 ; Martini 3 THIO model
1 3 1 0.270 ; Martini 3 THIO model
2 3 1 0.280 ; Martini 3 THIO model
; thiophene-propyl
3 4 1 0.285 ; [DOI:10.1021/jacs.6b11717]
[angles]
; i j k funct angle force_k
1 3 4 2 180 250 ; [DOI:10.1021/jacs.6b11717]
;;;;;; 4-METHYLIMIDAZOLE
;;;;; (amino acid HIStidine)
[moleculetype]
; molname nrexcl
4MIMI 1
[atoms]
; id type resnr residu atom cgnr charge
1 TN6d 1 4MIMI N1 1 0
2 TN5a 1 4MIMI N2 2 0
3 TC4 1 4MIMI R3 3 0
[constraints]
; i j funct length
1 2 1 0.270
2 3 1 0.300
1 3 1 0.320
;;;;;; 4-NITROANISOLE
[moleculetype]
; molname nrexcl
4NIAN 1
[atoms]
; id type resnr residu atom cgnr charge
1 SN3a 1 4NIAN N1 1 0
2 TC5 1 4NIAN R2 2 0
3 TC5 1 4NIAN R3 3 0
4 SN2a 1 4NIAN O4 4 0
[bonds]
; i j funct length
2 4 1 0.364 25000 ; cog
3 4 1 0.364 25000 ; cog
[constraints]
; i j funct length
1 2 1 0.366 ; cog
1 3 1 0.366 ; cog
2 3 1 0.337 ; cog
[dihedrals]
; i j k l funct ref.angle force_k
1 2 3 4 2 180.00 75
[exclusions]
1 4
;;;;;; ACETOPHENONE
;
; Reference(s):
; PCT Souza, S Thallmair, P Conflitti, JC Ramirez Palacios, R Alessandri, S Raniolo, V Limongelli, SJ Marrink, Protein-Ligand
; Binding with the Coarse-Grained Martini Model, Nat. Commun. 2020, 11, 3714, [DOI: 10.1038/s41467-020-17437-5].
;
; Note(s):
; Bead types updated to the Martini 3 parameters from the Martini 3 open-beta model [DOI: 10.1038/s41467-020-17437-5].
; For minimizations, you may use define=-DFLEXIBLE to use a stiff-bond version of the topology that is more amenable to minimization.
;
[moleculetype]
; molname nrexcl
ACPH 1
[atoms]
; id type resnr residu atom cgnr charge
1 SN4a 1 ACPH R1 1 0
2 TC5 1 ACPH R2 2 0
3 TC5 1 ACPH R3 3 0
4 TC5 1 ACPH R4 4 0
[bonds]
#ifndef FLEXIBLE
[constraints]
#endif
; i j funct length
1 2 1 0.319 1000000 ; cog
1 3 1 0.327 1000000 ; cog
2 3 1 0.285 1000000
2 4 1 0.285 1000000
3 4 1 0.285 1000000
[dihedrals]
; i j k l funct ref.angle force_k
1 2 3 4 2 180.00 25
[exclusions]
1 4
;;;;;; ANILINE
[moleculetype]
; molname nrexcl
ANIL 1
[atoms]
; id type resnr residu atom cgnr charge
1 SN6d 1 ANIL N1 1 0
2 TC5 1 ANIL R2 2 0
3 TC5 1 ANIL R3 3 0
[constraints]
; i j funct length
1 2 1 0.295
2 3 1 0.285
1 3 1 0.295
;;;;;; BENZALDEHYDE
;
; Note(s):
; For minimizations, you may use define=-DFLEXIBLE to use a stiff-bond version of the topology that is more amenable to minimization.
;
[moleculetype]
; molname nrexcl
BEAL 1
[atoms]
; id type resnr residu atom cgnr charge
1 TN4a 1 BEAL O1 1 0
2 TC5 1 BEAL R2 2 0
3 TC5 1 BEAL R3 3 0
4 TC5 1 BEAL R4 4 0
[bonds]
#ifndef FLEXIBLE
[constraints]
#endif
; i j funct length
1 2 1 0.316 1000000 ; cog
1 3 1 0.316 1000000 ; cog
2 3 1 0.290 1000000 ; cog
2 4 1 0.248 1000000 ; cog
3 4 1 0.248 1000000 ; cog
[dihedrals]
; i j k l funct ref.angle force_k
1 2 3 4 2 180.00 100
[exclusions]
1 4
;;;;;; BENZENE
[moleculetype]
; molname nrexcl
BENZ 1
[atoms]
; id type resnr residu atom cgnr charge
1 TC5 1 BENZ R1 1 0
2 TC5 1 BENZ R2 2 0
3 TC5 1 BENZ R3 3 0
[constraints]
; i j funct length
1 2 1 0.290 ; cog
2 3 1 0.290 ; cog
1 3 1 0.290 ; cog
;;;;;; 4-BROMOANISOLE
;
; Note(s):
; For minimizations, you may use define=-DFLEXIBLE to use a stiff-bond version of the topology that is more amenable to minimization.
;
[ moleculetype ]
; molname nrexcl
BRA 1
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 SN2a 1 BRA O1 1 0 54
2 TC5 1 BRA R2 2 0 36
3 TC5 1 BRA R3 3 0 36
4 TX2 1 BRA X4 4 0 36
[bonds]
#ifndef FLEXIBLE
[constraints]
#endif
; i j funct length
1 2 1 0.315 1000000 ; cog
1 3 1 0.315 1000000 ; cog
2 3 1 0.265 1000000 ; cog
2 4 1 0.330 1000000 ; cog
3 4 1 0.330 1000000 ; cog
[ dihedrals ]
; Keeping it flat using improper
; i j k l func angle strength
1 2 3 4 2 180 250
[ exclusions ]
; i j k l
1 4
;;;;;; BROMOBENZENE
[moleculetype]
; molname nrexcl
BRBZ 1
[atoms]
; id type resnr residu atom cgnr charge
1 SX2 1 BRBZ Br 1 0
2 TC5 1 BRBZ R2 2 0
3 TC5 1 BRBZ R3 3 0
[constraints]
; i j funct length
1 2 1 0.310 ; cog
2 3 1 0.290 ; cog
1 3 1 0.310 ; cog
;;;;;; 1,3-BENZENEDIOL
[moleculetype]
; molname nrexcl
BZDOL 1
[atoms]
; id type resnr residu atom cgnr charge
1 SN6 1 BZDOL O1 1 0
2 SN6 1 BZDOL O2 2 0
3 TC5 1 BZDOL R3 3 0
[constraints]
; i j funct length
1 2 1 0.325 ; cog
2 3 1 0.320 ; cog
1 3 1 0.320 ; cog
;;;;;; BENZONITRILE
;
; Note(s):
; For minimizations, you may use define=-DFLEXIBLE to use a stiff-bond version of the topology that is more amenable to minimization.
;
[moleculetype]
; molname nrexcl
BZNI 1
[atoms]
; id type resnr residu atom cgnr charge
1 TN4a 1 BZNI N1 1 0
2 TC5 1 BZNI R2 2 0
3 TC5 1 BZNI R3 3 0
4 TC5 1 BZNI R4 4 0
[bonds]
#ifndef FLEXIBLE
[constraints]
#endif
; i j funct length
1 2 1 0.298 1000000 ; cog
1 3 1 0.298 1000000 ; cog
2 3 1 0.290 1000000 ; cog (benzene)
2 4 1 0.290 1000000 ; cog (benzene)
3 4 1 0.290 1000000 ; cog (benzene)
[dihedrals]
; i j k l funct ref.angle force_k
1 2 3 4 2 180.00 100
[exclusions]
1 4
;;;;;; para-BENZOQUINONE
;
; Note(s):
; For minimizations, you may use define=-DFLEXIBLE to use a stiff-bond version of the topology that is more amenable to minimization.
;
[moleculetype]
; molname nrexcl
BZQU 1
[atoms]
; id type resnr residu atom cgnr charge
1 TN6a 1 BZQU O1 1 0
2 TC5 1 BZQU R2 2 0
3 TC5 1 BZQU R3 3 0
4 TN6a 1 BZQU O4 4 0
[bonds]
#ifndef FLEXIBLE
[constraints]
#endif
; i j funct length
1 2 1 0.268 1000000 ; cog
1 3 1 0.268 1000000 ; cog
2 3 1 0.344 1000000 ; cog
2 4 1 0.268 1000000 ; cog
3 4 1 0.268 1000000 ; cog
[dihedrals]
; i j k l funct ref.angle force_k
1 2 3 4 2 180.00 100
[exclusions]
1 4
;;;;;; BENZOTRIFLUORIDE (aka TRIFLUOROTOLUENE)
;
; Note(s):
; For minimizations, you may use define=-DFLEXIBLE to use a stiff-bond version of the topology that is more amenable to minimization.
;
[moleculetype]
; molname nrexcl
BZTF 1
[atoms]
; id type resnr residu atom cgnr charge
1 SX4e 1 BZTF F1 1 0
2 TC5 1 BZTF R2 2 0
3 TC5 1 BZTF R3 3 0
4 TC5 1 BZTF R4 4 0
[bonds]
#ifndef FLEXIBLE
[constraints]
#endif
; i j funct length
1 2 1 0.300 1000000 ;
1 3 1 0.300 1000000 ;
2 3 1 0.290 1000000 ; cog (benzene)
2 4 1 0.290 1000000 ; cog (benzene)
3 4 1 0.290 1000000 ; cog (benzene)
[dihedrals]
; i j k l funct ref.angle force_k
1 2 3 4 2 180.00 200
[exclusions]
1 4
;;;;;; CYCLOHEXANE
[moleculetype]
; molname nrexcl
CHEX 1
[atoms]
; id type resnr residu atom cgnr charge
1 SC3 1 CHEX R1 1 0
2 SC3 1 CHEX R2 2 0
[bonds]
; i j funct length force.c.
1 2 1 0.378 5000 ; cog
;;;;;; CYCLOHEXENE
[moleculetype]
; molname nrexcl
CHEXE 1
[atoms]
; id type resnr residu atom cgnr charge
1 SC4 1 CHEXE C1 1 0
2 SC3 1 CHEXE C2 2 0
[bonds]
; i j funct length force.c.
1 2 1 0.360 5000
;;;;;; CHLOROBENZENE
[moleculetype]
; molname nrexcl
CLBZ 1
[atoms]
; id type resnr residu atom cgnr charge
1 SX3 1 CLBZ Cl 1 0
2 TC5 1 CLBZ R2 2 0
3 TC5 1 CLBZ R3 3 0
[constraints]
; i j funct length
1 2 1 0.320
2 3 1 0.280
1 3 1 0.320
;;;;;; CHLORPROPHAM
;
; Note(s):
; Schematic of the model:
;
; TC5
; / \ __SC2
; SX3 SP2
; \ /
; TC5
;
[moleculetype]
; molname nrexcl
CLPR 1
[atoms]
;id type resnr residu atom cgnr charge
1 SX3 1 CLPR X1 1 0
2 TC5 1 CLPR R2 2 0
3 TC5 1 CLPR R3 3 0
4 SP2 1 CLPR O4 4 0
5 SC2 1 CLPR C5 5 0
[bonds]
; i j funct length force_k
2 4 1 0.408 25000 ; cog
3 4 1 0.272 25000 ; cog
4 5 1 0.321 25000 ; cog
[constraints]
; i j funct length
1 2 1 0.306 ; cog
1 3 1 0.264 ; cog
2 3 1 0.301 ; cog
[angles]
; i j k funct ref.angle force_k
2 4 5 1 155.0 100 ; cog
3 4 5 1 155.0 100 ; cog
[dihedrals]
; i j k l funct ref.angle force_k
1 2 3 4 2 180.00 50 ; planarity of ring + bead 4
4 2 3 5 2 0.00 50 ; position of bead 5 w.r.t. other beads
[exclusions]
1 4
;;;;;; 2-CHLOROTOLUENE
[moleculetype]
; molname nrexcl
CLTL 1
[atoms]
; id type resnr residu atom cgnr charge
1 SX3 1 CLTL Cl 1 0
2 SC4 1 CLTL R2 2 0
3 TC5 1 CLTL R3 3 0
[constraints]
; i j funct length
1 2 1 0.326 ; cog
2 3 1 0.377 ; cog
1 3 1 0.306 ; cog
;;;;;; CYCLOPROPANE
[moleculetype]
; molname nrexcl
CPR 1
[atoms]
; id type resnr residu atom cgnr charge
1 SC3 1 CPR R1 1 0
;;;;;; CUMENE
[moleculetype]
; molname nrexcl
CUME 1
[atoms]
; id type resnr residu atom cgnr charge
1 SC3 1 CUME R1 1 0
2 TC5 1 CUME R2 2 0
3 TC5 1 CUME R3 3 0
4 TC5 1 CUME R4 4 0
[bonds]
; i j funct length force.c.
1 2 1 0.310 20000 ; cog
1 3 1 0.310 20000 ; cog
[constraints]
; i j funct length
2 3 1 0.290 ; benzene
2 4 1 0.290 ; benzene
3 4 1 0.290 ; benzene
[dihedrals]
; i j k l funct ref.angle force_k
1 2 3 4 2 180.00 100
[exclusions]
1 4
;;;;;; CYCLOPENTANE
[moleculetype]
; molname nrexcl
CYPE 1
[atoms]
; id type resnr residu atom cgnr charge
1 TC3 1 CYPE C1 1 0
2 SC3 1 CYPE C2 2 0
[bonds]
; i j funct length force.c.
1 2 1 0.310 5000
;;;;;; CYCLOPENTANONE
[moleculetype]
; molname nrexcl
CYPO 1
[atoms]
; id type resnr residu atom cgnr charge
1 SC3 1 CYPO R1 1 0
2 TN6a 1 CYPO O2 2 0
[bonds]
; i j funct length force.c.
1 2 1 0.300 5000 ;
;;;;;; CYCLOPENTANOL
[moleculetype]
; molname nrexcl
CYPOL 1
[atoms]
; id type resnr residu atom cgnr charge
1 SN6 1 CYPOL O1 1 0
2 SC3 1 CYPOL R2 2 0
[bonds]
; i j funct length force.c.
1 2 1 0.331 5000 ; cog
;;;;;; 1,2-DIBROMOBENZENE OR 1,3-DIBROMOBENZENE
[moleculetype]
; molname nrexcl
DBRBZ 1
[atoms]
; id type resnr residu atom cgnr charge
1 SX2 1 DBRBZ Br 1 0
2 SX2 1 DBRBZ Br 2 0
3 TC5 1 DBRBZ R3 3 0
[constraints]
; i j funct length
1 2 1 0.318 ; cog average of 1,2- and 1,3-dibromobenzene
1 3 1 0.309 ; cog average of 1,2- and 1,3-dibromobenzene
2 3 1 0.309 ; cog average of 1,2- and 1,3-dibromobenzene
;;;;;; 1,2-DICHLOROBENZENE or 1,3-DICHLOROBENZENE
[moleculetype]
; molname nrexcl
DCLBZ 1
[atoms]
; id type resnr residu atom cgnr charge
1 SX3 1 DCLBZ R1 1 0
2 SX3 1 DCLBZ R2 2 0
3 TC5 1 DCLBZ R3 3 0
[constraints]
; i j funct length
1 2 1 0.324
1 3 1 0.316
2 3 1 0.316
;;;;;; 1,4-DIOXANE
[moleculetype]
; molname nrexcl
DIOX 1
[atoms]
; id type resnr residu atom cgnr charge
1 SN3a 1 DIOX O1 1 0
2 SN3a 1 DIOX O2 2 0
[bonds]
; i j funct length force.c.
1 2 1 0.300 5000
;;;;;; N,N-DIMETHYLANILINE
;
; Note(s):
; For minimizations, you may use define=-DFLEXIBLE to use a stiff-bond version of the topology that is more amenable to minimization.
;
[moleculetype]
; molname nrexcl
DMAN 1
[atoms]
; id type resnr residu atom cgnr charge
1 SN1 1 DMAN N1 1 0
2 TC5 1 DMAN R2 2 0
3 TC5 1 DMAN R3 3 0
4 TC5 1 DMAN R4 4 0
[bonds]
#ifndef FLEXIBLE
[constraints]
#endif
; i j funct length
1 2 1 0.330 1000000
1 3 1 0.330 1000000
2 3 1 0.285 1000000
2 4 1 0.285 1000000
3 4 1 0.285 1000000
[dihedrals]
; i j k l funct ref.angle force_k
1 2 3 4 2 180.00 100
[exclusions]
1 4
;;;;;; 2,5-DIMETHYL-1,4-BENZOQUINONE
;
; Note(s):
; For minimizations, you may use define=-DFLEXIBLE to use a stiff-bond version of the topology that is more amenable to minimization.
;
[moleculetype]
; molname nrexcl
DMBZQ 1
[atoms]
; id type resnr residu atom cgnr charge
1 TN6a 1 DMBZQ O1 1 0
2 SC4 1 DMBZQ R2 2 0
3 SC4 1 DMBZQ R3 3 0
4 TN6a 1 DMBZQ O4 4 0
[bonds]
#ifndef FLEXIBLE
[constraints]
#endif
; i j funct length
1 2 1 0.359 1000000 ; cog
1 3 1 0.263 1000000 ; cog
2 3 1 0.477 1000000 ; cog
2 4 1 0.263 1000000 ; cog
3 4 1 0.359 1000000 ; cog
[dihedrals]
; i j k l funct ref.angle force_k
1 2 3 4 2 180.00 100
[exclusions]
1 4
;;;;;; 1,3-DIOXOLANE
[moleculetype]
; molname nrexcl
DXLA 1
[atoms]
; id type resnr residu atom cgnr charge
1 TC3 1 DXLA O1 1 0
2 SN5a 1 DXLA O2 2 0
[bonds]
; i j funct length force.c.
1 2 1 0.253 5000 ; cog
;;;;;; ETHYL-BENZENE
;
; Reference(s):
; PCT Souza, S Thallmair, P Conflitti, JC Ramirez Palacios, R Alessandri, S Raniolo, V Limongelli, SJ Marrink, Protein-Ligand
; Binding with the Coarse-Grained Martini Model, Nat. Commun. 2020, 11, 3714, [DOI: 10.1038/s41467-020-17437-5].
;
; Note(s):
; Bead types updated to the Martini 3 parameters from the Martini 3 open-beta model [DOI: 10.1038/s41467-020-17437-5].
; For minimizations, you may use define=-DFLEXIBLE to use a stiff-bond version of the topology that is more amenable to minimization.
;
[moleculetype]
; molname nrexcl
EBEN 1
[atoms]
; id type resnr residu atom cgnr charge
1 TC5 1 EBEN R1 1 0
2 TC5 1 EBEN R2 2 0
3 TC5 1 EBEN R3 3 0
4 TC3 1 EBEN R4 4 0
[bonds]
#ifndef FLEXIBLE
[constraints]
#endif
; i j funct length
1 2 1 0.291 1000000
1 3 1 0.291 1000000
2 3 1 0.291 1000000
2 4 1 0.320 1000000
3 4 1 0.320 1000000
[dihedrals]
; i j k l funct ref.angle force_k
1 2 3 4 2 180.00 100
[ exclusions ]
1 4
;;;;;; FURAN
[moleculetype]
; molname nrexcl
FURA 1
[atoms]
; id type resnr residu atom cgnr charge
1 TN2a 1 FURA O1 1 0
2 TC5 1 FURA R2 2 0
3 TC5 1 FURA R3 3 0
[constraints]
; i j funct length
1 2 1 0.240
2 3 1 0.260
1 3 1 0.240
;;;;;; IMIDAZOLE
[moleculetype]
; molname nrexcl
IMID 1
[atoms]
; id type resnr residu atom cgnr charge
1 TN5a 1 IMID N1 1 0
2 TN6d 1 IMID N2 2 0
3 TC5 1 IMID R3 3 0
[constraints]
; i j funct length
1 2 1 0.265
2 3 1 0.270
1 3 1 0.265
;;;;;; IODOBENZENE
[moleculetype]
; molname nrexcl
IOBZ 1
[atoms]
; id type resnr residu atom cgnr charge
1 X1 1 IOBZ I 1 0
2 TC5 1 IOBZ R2 2 0
3 TC5 1 IOBZ R3 3 0
[constraints]
; i j funct length