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martini21bmw.py
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\#!/usr/bin/env python
import sys
version = "1.1"
tag = "20120826-TAW"
# Martini Force Field Definition Generating Script - BMW version
# Version 2012-02-19 TAW
# If a file with nonbonded parameters (atom types and interactions)
# is given on the command line, the output will be a merged forcefield
aa = len(sys.argv) > 1 and open(sys.argv[1]).readlines()
beads = { # Name: Mass
"P5": 72, "P4": 72, "P3": 72, "P2": 72, "P1": 72, # Polar
"Nda": 72, "Nd": 72, "Na": 72, "N0": 72, # Intermediate
"C5": 72, "C4": 72, "C3": 72, "C2": 72, "C1": 72, # Apolar
"Qda": 72, "Qd": 72, "Qa": 72, "Q0": 72, # Charged
"SP5": 45, "SP4": 45, "SP3": 45, "SP2": 45, "SP1": 45, # Ring type, polar
"SNda": 45, "SNd": 45, "SNa": 45, "SN0": 45, # Ring type, intermediate
"SC5": 45, "SC4": 45, "SC3": 45, "SC2": 45, "SC1": 45, # Ring type, apolar
"SQda": 45, "SQd": 45, "SQa": 45, "SQ0": 45, # Ring type, charged
"AC1": 72, "AC2": 72, # Amino acid side chains (Q-C interactions)
"RQd": 72, "AQa": 72, # BMW charged types
"BMC": 72, "BMQ": 72, # BMW water beads
}
martini_v2_1 ="""
; MARTINI FORCEFIELD V2.1 - FINAL VERSION WITH ADAPTATIONS FOR BMW WATER MODEL
;
; SJ MARRINK, 16-06-2007 (last modified: 26-1-2011)
;
; please cite:
;
; L. Monticelli, S. Kandasamy, X. Periole, R. Larson, D.P. Tieleman, S.J. Marrink.
; The MARTINI coarse grained force field: extension to proteins.
; J. Chem. Th. Comp., 4:819-834, 2008.
;
; S.J. Marrink, H.J. Risselada, S. Yefimov, D.P. Tieleman, A.H. de Vries.
; The MARTINI forcefield: coarse grained model for biomolecular simulations.
; JPC-B, 111:7812-7824, 2007.
;
; and (if using lipid topologies):
;
; S.J. Marrink, A.H. de Vries, A.E. Mark.
; Coarse grained model for semi-quantitative lipid simulations.
; JPC-B, 108:750-760, 2004.
[ defaults ]
1 1
[ atomtypes ]
; Currently eighteen main particle types are defined,
; divided into four main categories:
; (P, polar; N, intermediate; C, apolar; Q, charged)
; each of which has a number of sublevels (0,a,d, or ad)
; subtype 0 has no hydrogen bond forming capacities,
; subtype d has hydrogen donor capacities,
; subtype a has hydrogen acceptor capacities,
; and subtype da has both donor and acceptor capacities
; or (1,2,3,4,5) where subtype 5 is more polar than 1.
; Two main classes of particles are furthermore distinguished, namely
; STANDARD particles which are mapped using a 4:1 mapping scheme, and
; RING particles which are used for ring compounds mapped 2-3:1.
; A special BIG particle type is defined in addition to prevent freezing of CG water.
; Two AMINO acid particle types are used to avoid Q-C clashes inside proteins.
; For reasons of computational efficiency, all particle masses are set to 72 amu,
; except for ring types which are set to 45 amu.
; For realistic dynamics, the particle masses should be adapted.
; This might require a reduction of the integration timestep, however.
; name mass charge ptype c6 c12
"""
# Epsilon: 5.60(A), 5.00(B), 4.50(C), 4.00(D), 3.50(E), 3.10(F), 2.70(G), 2.30(H), 2.00(I)
# Sigma: 0.00(0), 0.43(1), 0.47(2), 0.57(3), 0.62(4)
# Scaling: 1.00(a), 0.95(b), 0.90(c), 0.75(d), 0.71(e)
epsilon = {
"0":0.00, # no interaction
"A":5.60, # supra attractive
"B":5.00, # attractive
"C":4.50, # almost attractive
"D":4.00, # semi attractive
"E":3.50, # intermediate
"F":3.10, # almost intermediate
"G":2.70, # semi repulsive
"H":2.30, # almost repulsive
"I":2.00, # repulsive
"Z":0.25, # with sigma=1 yields c6=12=1
}
sigma = {
"0":0.00, # no interaction
"1":0.43, # ring bead type
"2":0.47, # default bead type
"3":0.57, # supra attractive bead type
"4":0.62, # super repulsive bead type
"5":1.00, # unity: c6/12 parity
}
scale = {
"a":1.00, # no scaling
"b":0.95, # 95%: interaction with polarizable water
"c":0.90, # 90%: S* - C1 interactions with BMW water
"d":0.75, # 75%: ring bead types (S*) and uncharged interactions with BMW for epsilon >=4.5
"e":0.71, # 71%: uncharged interactions with BMW for epsilon<4.5
}
# BEAD TYPES
# Default bead types; 4:1 mapping, 72 AMU
plain = {
"P5": 72, "P4": 72, "P3": 72, "P2": 72, "P1": 72, # Polar
"Nda": 72, "Nd": 72, "Na": 72, "N0": 72, # Intermediate
"C5": 72, "C4": 72, "C3": 72, "C2": 72, "C1": 72, # Apolar
"Qda": 72, "Qd": 72, "Qa": 72, "Q0": 72, # Charged
"AC1": 72, "AC2": 72, # Amino acid specific (Q-C interactions)
}
# Ring bead types; mapping 2:1 or 3:1, 45 AMU
small = {
"SP5": 45, "SP4": 45, "SP3": 45, "SP2": 45, "SP1": 45, # Ring type, polar
"SNda": 45, "SNd": 45, "SNa": 45, "SN0": 45, # Ring type, intermediate
"SC5": 45, "SC4": 45, "SC3": 45, "SC2": 45, "SC1": 45, # Ring type, apolar
"SQda": 45, "SQd": 45, "SQa": 45, "SQ0": 45, # Ring type, charged
}
# Virtual sites, plain type; mapping 4:1, no mass
vsite = {
"vP5": 0, "vP4": 0, "vP3": 0, "vP2": 0, "vP1": 0, # Polar
"vNda": 0, "vNd": 0, "vNa": 0, "vN0": 0, # Intermediate
"vC5": 0, "vC4": 0, "vC3": 0, "vC2": 0, "vC1": 0, # Apolar
"vQda": 0, "vQd": 0, "vQa": 0, "vQ0": 0, # Charged
"vAC1": 0, "vAC2": 0, # Amino acid specific (Q-C interactions)
}
# Virtual sites, small type; mapping 2:1 or 3:1, no mass
svste = {
"vSP5": 0, "vSP4": 0, "vSP3": 0, "vSP2": 0, "vSP1": 0, # Ring type, polar
"vSNda": 0, "vSNd": 0, "vSNa": 0, "vSN0": 0, # Ring type, intermediate
"vSC5": 0, "vSC4": 0, "vSC3": 0, "vSC2": 0, "vSC1": 0, # Ring type, apolar
"vSQda": 0, "vSQd": 0, "vSQa": 0, "vSQ0": 0, # Ring type, charged
}
# Other: Special purpose types
other = {
"BP4": 72, # Big water particle (antifreeze). Not used with BMW
"D": 0, # Dummy particle type
"BMC": 72, # BMW water model central bead
"BMQ": 0, # BMW water model satellite
"RQd": 72, # BMW guanidinium group (Arginine)
"AQa": 72, # BMW negative bead
}
classes = ("plain","small","vsite","svste","other")
# Dummy atom types. These will be given a repulsion "DUMMY_REPEL"
# with all atoms from the atomistic forcefield, if provided
dummy = ["D","BMQ"]
# Gather all atom types
all,mass = zip(*[i for j in classes for i in eval(j).items()])
virtual = vsite.keys) + svste.keys()
rla = range(len(all))
cmb = [ (all[i],all[j]) for i in rla for j in rla[i:] ]
table_plain = """
Qda Qd Qa Q0 P5 P4 P3 P2 P1 Nda Nd Na N0 C5 C4 C3 C2 C1
Qda A A A C A A A B B A A A E D E E E E
Qd A B A C A A A B B A D A E D E E E E
Qa A A B C A A A B B A A D E D E E E E
Q0 C C C E B A B C D D D D E D E E E E
P5 A A A B A A A A A A A A E F G G H I
P4 A A A A A B B C C D A A A F G G H I
P3 A A A B A B B C C C C C E E F F G H
P2 B B B C A C C C C C C C D E E F G H
P1 B B B D A C C C C C C C D E E E F G
Nda A A A D A A C C C C C C E E F G G G
Nd A D A D A A C C C C D C E E F G G G
Na A A D D A A C C C C C D E E F G G G
N0 E E E E E E E D D E E E E E E E F G
C5 D D D D F F E E E E E E E E E E F F
C4 E E E E G G F E E F F F E E E E F F
C3 E E E E G G F F E G G G E E E E E E
C2 E E E E H H G G F G G G F F F E E E
C1 E E E E I I H H G G G G G F F E E E
"""
table_small = """
SQda SQd SQa SQ0 SP5 SP4 SP3 SP2 SP1 SNda SNd SNa SN0 SC5 SC4 SC3 SC2 SC1
SQda A1d A1d A1d C1d A1d A1d A1d B1d B1d A1d A1d A1d E1d D1d E1d E1d E1d E1d
SQd A1d B1d A1d C1d A1d A1d A1d B1d B1d A1d D1d A1d E1d D1d E1d E1d E1d E1d
SQa A1d A1d B1d C1d A1d A1d A1d B1d B1d A1d A1d D1d E1d D1d E1d E1d E1d E1d
SQ0 C1d C1d C1d E1d B1d A1d B1d C1d D1d D1d D1d D1d E1d D1d E1d E1d E1d E1d
SP5 A1d A1d A1d B1d A1d A1d A1d A1d A1d B1d B1d B1d E1d F1d G1d G1d H1d I1d
SP4 A1d A1d A1d A1d A1d B1d B1d C1d C1d D1d D1d D1d A1d F1d G1d G1d H1d I1d
SP3 A1d A1d A1d B1d A1d B1d B1d C1d C1d C1d C1d C1d E1d E1d F1d F1d G1d H1d
SP2 B1d B1d B1d C1d A1d C1d C1d C1d C1d C1d C1d C1d D1d E1d E1d F1d G1d H1d
SP1 B1d B1d B1d D1d A1d C1d C1d C1d C1d C1d C1d C1d D1d E1d E1d E1d F1d G1d
SNda A1d A1d A1d D1d B1d D1d C1d C1d C1d C1d C1d C1d E1d E1d F1d G1d G1d G1d
SNd A1d D1d A1d D1d B1d D1d C1d C1d C1d C1d D1d C1d E1d E1d F1d G1d G1d G1d
SNa A1d A1d D1d D1d B1d D1d C1d C1d C1d C1d C1d D1d E1d E1d F1d G1d G1d G1d
SN0 E1d E1d E1d E1d E1d E1d E1d D1d D1d E1d E1d E1d E1d E1d E1d E1d F1d G1d
SC5 D1d D1d D1d D1d F1d F1d E1d E1d E1d E1d E1d E1d E1d E1d E1d E1d F1d F1d
SC4 E1d E1d E1d E1d G1d G1d F1d E1d E1d F1d F1d F1d E1d E1d E1d E1d F1d F1d
SC3 E1d E1d E1d E1d G1d G1d F1d F1d E1d G1d G1d G1d E1d E1d E1d E1d E1d E1d
SC2 E1d E1d E1d E1d H1d H1d G1d G1d F1d G1d G1d G1d F1d F1d F1d E1d E1d E1d
SC1 E1d E1d E1d E1d I1d I1d H1d H1d G1d G1d G1d G1d G1d F1d F1d E1d E1d E1d
"""
table_small_plain = """
Qda Qd Qa Q0 P5 P4 P3 P2 P1 Nda Nd Na N0 C5 C4 C3 C2 C1
SQda A A A C A A A B B A A A E D E E E Ec
SQd A B A C A A A B B A D A E D E E E Ec
SQa A A B C A A A B B A A D E D E E E Ec
SQ0 C C C E B A B C D D D D E D E E E Ec
SP5 A A A B A A A A A A A A E F G G H Ic
SP4 A A A A A B B C C D A A A F G G H Ic
SP3 A A A B A B B C C C C C E E F F G Hc
SP2 B B B C A C C C C C C C D E E F G Hc
SP1 B B B D A C C C C C C C D E E E F Gc
SNda A A A D A A C C C C C C E E F G G Gc
SNd A D A D A A C C C C D C E E F G G Gc
SNa A A D D A A C C C C C D E E F G G Gc
SN0 E E E E E E E D D E E E E E E E F Gc
SC5 D D D D F F E E E E E E E E E E F Fc
SC4 E E E E G G F E E F F F E E E E F Fc
SC3 E E E E G G F F E G G G E E E E E Ec
SC2 E E E E H H G G F G G G F F F E E Ec
SC1 E E E E I I H H G G G G G F F E E Ec
"""
table_vsite_plain = """
Qda Qd Qa Q0 P5 P4 P3 P2 P1 Nda Nd Na N0 C5 C4 C3 C2 C1
vQda A A A C A A A B B A A A E D E E E E
vQd A B A C A A A B B A D A E D E E E E
vQa A A B C A A A B B A A D E D E E E E
vQ0 C C C E B A B C D D D D E D E E E E
vP5 A A A B A A A A A A A A E F G G H I
vP4 A A A A A B B C C D A A A F G G H I
vP3 A A A B A B B C C C C C E E F F G H
vP2 B B B C A C C C C C C C D E E F G H
vP1 B B B D A C C C C C C C D E E E F G
vNda A A A D A A C C C C C C E E F G G G
vNd A D A D A A C C C C D C E E F G G G
vNa A A D D A A C C C C C D E E F G G G
vN0 E E E E E E E D D E E E E E E E F G
vC5 D D D D F F E E E E E E E E E E F F
vC4 E E E E G G F E E F F F E E E E F F
vC3 E E E E G G F F E G G G E E E E E E
vC2 E E E E H H G G F G G G F F F E E E
vC1 E E E E I I H H G G G G G F F E E E
"""
table_small_vsite = """
vQda vQd vQa vQ0 vP5 vP4 vP3 vP2 vP1 vNda vNd vNa vN0 vC5 vC4 vC3 vC2 vC1
SQda A A A C A A A B B A A A E D E E E Ec
SQd A B A C A A A B B A D A E D E E E Ec
SQa A A B C A A A B B A A D E D E E E Ec
SQ0 C C C E B A B C D D D D E D E E E Ec
SP5 A A A B A A A A A A A A E F G G H Ic
SP4 A A A A A B B C C D A A A F G G H Ic
SP3 A A A B A B B C C C C C E E F F G Hc
SP2 B B B C A C C C C C C C D E E F G Hc
SP1 B B B D A C C C C C C C D E E E F Gc
SNda A A A D A A C C C C C C E E F G G Gc
SNd A D A D A A C C C C D C E E F G G Gc
SNa A A D D A A C C C C C D E E F G G Gc
SN0 E E E E E E E D D E E E E E E E F Gc
SC5 D D D D F F E E E E E E E E E E F Fc
SC4 E E E E G G F E E F F F E E E E F Fc
SC3 E E E E G G F F E G G G E E E E E Ec
SC2 E E E E H H G G F G G G F F F E E Ec
SC1 E E E E I I H H G G G G G F F E E Ec
"""
table_svste_plain = """
Qda Qd Qa Q0 P5 P4 P3 P2 P1 Nda Nd Na N0 C5 C4 C3 C2 C1
vSQda A A A C A A A B B A A A E D E E E Ec
vSQd A B A C A A A B B A D A E D E E E Ec
vSQa A A B C A A A B B A A D E D E E E Ec
vSQ0 C C C E B A B C D D D D E D E E E Ec
vSP5 A A A B A A A A A A A A E F G G H Ic
vSP4 A A A A A B B C C D A A A F G G H Ic
vSP3 A A A B A B B C C C C C E E F F G Hc
vSP2 B B B C A C C C C C C C D E E F G Hc
vSP1 B B B D A C C C C C C C D E E E F Gc
vSNda A A A D A A C C C C C C E E F G G Gc
vSNd A D A D A A C C C C D C E E F G G Gc
vSNa A A D D A A C C C C C D E E F G G Gc
vSN0 E E E E E E E D D E E E E E E E F Gc
vSC5 D D D D F F E E E E E E E E E E F Fc
vSC4 E E E E G G F E E F F F E E E E F Fc
vSC3 E E E E G G F F E G G G E E E E E Ec
vSC2 E E E E H H G G F G G G F F F E E Ec
vSC1 E E E E I I H H G G G G G F F E E Ec
"""
table_svste_small = """
SQda SQd SQa SQ0 SP5 SP4 SP3 SP2 SP1 SNda SNd SNa SN0 SC5 SC4 SC3 SC2 SC1
vSQda A1d A1d A1d C1d A1d A1d A1d B1d B1d A1d A1d A1d E1d D1d E1d E1d E1d E1d
vSQd A1d B1d A1d C1d A1d A1d A1d B1d B1d A1d D1d A1d E1d D1d E1d E1d E1d E1d
vSQa A1d A1d B1d C1d A1d A1d A1d B1d B1d A1d A1d D1d E1d D1d E1d E1d E1d E1d
vSQ0 C1d C1d C1d E1d B1d A1d B1d C1d D1d D1d D1d D1d E1d D1d E1d E1d E1d E1d
vSP5 A1d A1d A1d B1d A1d A1d A1d A1d A1d B1d B1d B1d E1d F1d G1d G1d H1d I1d
vSP4 A1d A1d A1d A1d A1d B1d B1d C1d C1d D1d D1d D1d A1d F1d G1d G1d H1d I1d
vSP3 A1d A1d A1d B1d A1d B1d B1d C1d C1d C1d C1d C1d E1d E1d F1d F1d G1d H1d
vSP2 B1d B1d B1d C1d A1d C1d C1d C1d C1d C1d C1d C1d D1d E1d E1d F1d G1d H1d
vSP1 B1d B1d B1d D1d A1d C1d C1d C1d C1d C1d C1d C1d D1d E1d E1d E1d F1d G1d
vSNda A1d A1d A1d D1d B1d D1d C1d C1d C1d C1d C1d C1d E1d E1d F1d G1d G1d G1d
vSNd A1d D1d A1d D1d B1d D1d C1d C1d C1d C1d D1d C1d E1d E1d F1d G1d G1d G1d
vSNa A1d A1d D1d D1d B1d D1d C1d C1d C1d C1d C1d D1d E1d E1d F1d G1d G1d G1d
vSN0 E1d E1d E1d E1d E1d E1d E1d D1d D1d E1d E1d E1d E1d E1d E1d E1d F1d G1d
vSC5 D1d D1d D1d D1d F1d F1d E1d E1d E1d E1d E1d E1d E1d E1d E1d E1d F1d F1d
vSC4 E1d E1d E1d E1d G1d G1d F1d E1d E1d F1d F1d F1d E1d E1d E1d E1d F1d F1d
vSC3 E1d E1d E1d E1d G1d G1d F1d F1d E1d G1d G1d G1d E1d E1d E1d E1d E1d E1d
vSC2 E1d E1d E1d E1d H1d H1d G1d G1d F1d G1d G1d G1d F1d F1d F1d E1d E1d E1d
vSC1 E1d E1d E1d E1d I1d I1d H1d H1d G1d G1d G1d G1d G1d F1d F1d E1d E1d E1d
"""
table_other = """
D BMC BMQ RQd AQa
D 0 0 0 0 0
BMC 0 Z5 0 E B
BMQ 0 0 0 0 0
RQd 0 E 0 B A
AQa 0 B 0 A B
"""
table_other_plain = """
Qda Qd Qa Q0 P5 P4 P3 P2 P1 Nda Nd Na N0 C5 C4 C3 C2 C1
D 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
BMC B B B B Ad Bd Bd Cd Cd De De De Ee Fe Ge Ge He Ie
BMQ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
RQd A B A C A A A B B A D A E D E E E E
AQa A A B C A A A B B A A D E D A A A A
"""
table_other_small = """
SQda SQd SQa SQ0 SP5 SP4 SP3 SP2 SP1 SNda SNd SNa SN0 SC5 SC4 SC3 SC2 SC1
D 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
BMC B B B B Ad Bd Bd Cd Cd De De De Ee Fe Ge Ge He Ie
BMQ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
RQd A B A C A A A B B A D A E D E E E E
AQa A A B C A A A B B A A D E D A A A A
"""
table_other_vsite = """
vQda vQd vQa vQ0 vP5 vP4 vP3 vP2 vP1 vNda vNd vNa vN0 vC5 vC4 vC3 vC2 vC1
D 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
BMC B B B B Ad Bd Bd Cd Cd De De De Ee Fe Ge Ge He Ie
BMQ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
RQd A B A C A A A B B A D A E D E E E E
AQa A A B C A A A B B A A D E D A A A A
"""
table_other_svste = """
vSQda vSQd vSQa vSQ0 vSP5 vSP4 vSP3 vSP2 vSP1 vSNda vSNd vSNa vSN0 vSC5 vSC4 vSC3 vSC2 vSC1
D 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
BMC B B B B Ad Bd Bd Cd Cd De De De Ee Fe Ge Ge He Ie
BMQ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
RQd A B A C A A A B B A D A E D E E E E
AQa A A B C A A A B B A A D E D A A A A
"""
def table2pairs(x):
labels2 = x.pop(0)
return [((i[0],j),k) for i in x for j,k in zip(labels2,i[1:])]
def sigeps2c(eps=None,scl="a",sig="2"):
"""
Convert a string encoding for epsilon, sigma and scaling to C6 and C12 parameters
"""
if eps == None:
return None,None
if scl in sigma.keys():
sig, scl = scl, "2"
return 4*epsilon[eps]*scale[scl]*sigma[sig]**6, 4*epsilon[eps]*scale[scl]*sigma[sig]**12
tables = []
for i in classes:
tables.append(globals().get("table_%s"%i))
for j in classes:
tables.append(globals().get("table_%s_%s"%(i,j)))
tables = [[ j.split() for j in i.split("\n") if j not in ("","\n") ] for i in tables if i]
pairs = dict([j for i in tables for j in table2pairs(i)])
## -- Prepare the output
atomtypes = []
nonbond_params = []
pairtypes = []
# Read in atomistic stuff
if len(sys.argv) > 1:
aa = open(sys.argv[1]).readlines()
key = ""
atomtypes.append("; Atomistic definitions\n")
nonbond_params.append("; Atomistic definitions\n")
pairtypes.append("; Atomistic definitions\n")
for line in aa:
s = line.strip()
if s and s[0] == "[":
key=line
elif "nonbond_params" in key:
nonbond_params.append(line)
elif "atomtypes" in key:
atomtypes.append(line)
elif "pairtypes" in key:
pairtypes.append(line)
atomtypes.append("; End of atomistic definitions\n")
nonbond_params.append("; End of atomistic definitions\n")
pairtypes.append("; End of atomistic definitions\n")
# Note which atomtypes we have for defining interactions with dummy particles
aa_atomtypes = [i.split()[0] for i in atomtypes if i.strip() and not i.strip()[0] == ";"]
# Add coarsegrained stuff
typestr="%5s 0 %10.3f 0.000 %1s 0.0 0.0\n"
atomtypes.extend([typestr%(tp,ms,tp in virtual and 'V' or 'A') for tp,ms in zip(all,mass)])
for i,j in cmb:
c6,c12 = sigeps2c(*pairs.get((i,j),pairs.get((j,i),"")))
if c6:
nonbond_params.append(" %7s %7s %2d %e %e\n"%(i,j,1,c6,c12))
atomtypes.append("; End of coarsegrained definitions\n")
if nonbond_params:
nonbond_params.append("; End of coarsegrained definitions\n")
if pairtypes:
pairtypes.append("; End of coarsegrained definitions\n")
for i in dummy:
if i in tp:
for j in aa_atomtypes:
nonbond_params.append(" %7s %7s %2d 0.0 DUMMY_REPEL\n"%(i,j,1))
# Print stuff:
print "; This file was created automagically by", sys.argv[0]
print "; (c)2012 Tsjerk A Wassenaar, University of Groningen"
print ";"
if len(sys.argv) > 1:
print "; This file contains a merged forcefield, combining %s with MARTINI" % sys.argv[1]
print ";"
print "#define DUMMY_REPEL 1e-7"
print ";"
print martini_v2_1
print "".join(atomtypes), "\n"
print "[ nonbond_params ]\n", "".join(nonbond_params), "\n"
if pairtypes:
print "[ pairtypes ]\n", "".join(pairtypes), "\n"
print
for i in sys.argv[2:]: print open(i).read()