1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
|
#!/usr/bin/env python2
# usage: make_gromos_rtp.py > ffG43a1.rtp
# this script tries to make a residue topology database for GROMACS from
# the GROMOS version of this file. It needs ffG43a1.atp to fill in the
# atom types for the atom integer codes. It converts until it finds the string
# "#RNMES", which indicates the start of the solvent part
# of mtb43a1.dat. Solvents are treated differently in GROMACS
# The vaiables GROMOS_FILE and ATOMTYPE_FILE has to be specified as required.
# The output file requires some manual modifications:
# add ACE and NH2
# add 4 dihedrals with parameters 0 0 2 in HEME
# remove I in front of all atoms names in SO42-
# make a copy of H2O called HOH
# author: Klaas Dijkstra, Univ. Groningen
# Oct. 2000
# minor modifications by Berk Hess
from string import atoi, split
GROMOS_FILE = 'mtb43a1.dat'
ATOMTYPE_FILE = 'ffG43a1.atp'
START = '# RNME\012'
STOP = '#RNMES\012'
NATOM = '# NMAT,NLIN\012'
EXCLUS = '#ATOM MAE MSAE\012'
ATOM1 = '#ATOM ANM IACM MASS CGMICGM MAE MSAE\012'
ATOM2 = '#ATOM ANM IACM MASS CGM ICGM MAE MSAE\012'
ATOMtr = '#ATOM ANM IACM MASS CGMICGM\012'
NB = '# NB\012'
NBA = '# NBA\012'
NIDA = '# NIDA\012'
NDA = '# NDA\012'
#### functions
def translate(t): # translate number into atom code
if t == 0 : t = '-O'
elif t == -1 : t = '-C'
elif t == -2 : t = '-CA'
elif t == f.natom+1 : t = '+N'
else : t = f.atoms[t-1][1]
return t
def findbonds(atomnumber):
atom = eval(f.atoms[atomnumber][0])
onebond = []
twobond = []
ext = []
bond = []
ind = []
excl = []
for i in f.bonds:
a, b = i[0:2]
bond.append(eval(a),eval(b))
bond.append(eval(b),eval(a))
for i in bond:
if i[0] == atom: onebond.append(i[1])
for i in bond:
for j in onebond:
if i[0] == j and atom < i[1]: twobond.append(i[1])
ext = onebond
ext.extend(twobond)
for i in ext:
if i<atom:
ind.append(i)
for i in ind:
ext.remove(i)
ext.sort()
for i in ext:
excl.append(`i`)
return excl
#### general class to unravel a gromos topology file
class Cin:
def __init__(self, filename):
f=open(filename)
self.G = open(filename).readlines()
self.nlines = len(self.G)
def index(self):
" Find all indexes of lines with string '# RNME\012'and '#RNMES\012' "
self.ind = []
for i in range(self.nlines):
if self.G[i] == STOP:
self.ind.append(i)
return
if self.G[i] == START:
self.ind.append(i)
def mkres(self):
" Returns list of residues "
self.all = []
length = len(self.ind)
for i in range(length):
res = []
start = self.ind[i] + 1
try: stop = self.ind[i+1] - 2
except: return
for j in range(start,stop):
res.append(self.G[j])
self.all.append(res)
def gets(self,list,string):
" Returns linenumber of string in list"
for i in range(len(list)):
if list[i] == string:
return i
print >> sys.stderr, "Could not find string", string, "in list of length", len(list)
return -1
#--------------------------#
# unravel gromos list
def getRESname(self, res):
" Get the name of the current residue "
self.residue = split(res[0])
def getNATOM(self, res):
" Get number of atoms, number of preceding excl. "
ind = self.gets(res, NATOM)
self.natom, self.nlin = split(res[ind+1])
self.natom = atoi(self.natom)
self.nlin = atoi(self.nlin)
def getEXCLUS(self, res):
" Get preceding exclusions "
self.exclus = []
ind = self.gets(res, EXCLUS)
for i in range(self.nlin):
self.exclus.append(split(res[ind+i+1]))
def getATOM(self, res):
" Get atoms"
self.atoms = []
try: ind = self.gets(res, ATOM1)
except: ind = self.gets(res, ATOM2)
i = 0
cntr = 0
while cntr < self.natom - self.nlin:
i = i + 1
line = split(res[ind+i]) # get next line
noflo = (atoi(line[6])-1)/8 # if MAE > 8 cont. on next line
if noflo < 0: noflo = 0
for j in range(noflo):
i = i + 1
line1 = split(res[ind+i]) # overflow line
"print line1"
line = line + line1
self.atoms.append(line)
cntr = cntr + 1
def getATOMtr(self, res):
" Get trailing atoms"
self.atomtr = []
try: ind = self.gets(res, ATOMtr)
except: return
for i in range(self.nlin):
self.atomtr.append(split(res[ind+i+1]))
self.atoms.append(split(res[ind+i+1]))
def getBOND(self, res):
" Get bonds"
self.bonds = []
ind = self.gets(res, NB)
self.nb = atoi(split(res[ind+1])[0])
j = 0
for i in range(self.nb):
line = split(res[ind+i+j+3])
if line[0] == '#':
line = split(res[ind+i+j+4])
j = j+1
self.bonds.append(line)
def getNBA(self, res):
" Get bond angles"
self.ba = []
ind = self.gets(res, NBA)
self.nba = atoi(split(res[ind+1])[0])
j = 0
for i in range(self.nba):
line = split(res[ind+i+j+3])
if line[0] == '#':
line = split(res[ind+i+j+4])
j = j + 1
self.ba.append(line)
def getNIDA(self, res):
" Get improper dihedrals"
self.ida = []
ind = self.gets(res, NIDA)
self.nida = atoi(split(res[ind+1])[0])
j = 0
for i in range(self.nida):
line = split(res[ind+i+j+3])
if line[0] == '#':
line = split(res[ind+i+j+4])
j = j + 1
self.ida.append(line)
def getNDA(self, res):
" Get dihedrals"
self.da = []
ind = self.gets(res, NDA)
j = 0
self.nda = atoi(split(res[ind+1])[0])
for i in range(self.nda):
line = split(res[ind+i+j+3])
if line[0] == '#':
line = split(res[ind+i+j+4])
j = j + 1
self.da.append(line)
#-----------------------------#
# main program
typ = open(ATOMTYPE_FILE) # translate numbers to atoms
typelines = typ.readlines()
for i in range(len(typelines)):
typelines[i]=split(typelines[i])
f=Cin(GROMOS_FILE) # bind class instance
f.index() # mark all residues (f.ind)
f.mkres() # put all residues into list (f.all)
start = 0; stop = 92
" The rtp header "
print "[ bondedtypes ]"
print "; bonds angles dihedrals impropers"
print " 2 2 1 2"
for resnum in range(start,stop): # loop through all residues
f.getRESname(f.all[resnum]) # residue name
f.getNATOM (f.all[resnum]) # number of atoms
if f.nlin != 0: # 0 for a separate molecule
f.getEXCLUS(f.all[resnum]) # number of exclusions
f.getATOM (f.all[resnum]) # atoms => f.atoms
f.getATOMtr (f.all[resnum]) # trailing atoms => f.atomtr
f.getBOND (f.all[resnum]) # bonds => f.bonds
f.getNBA (f.all[resnum]) # bond angles => f.ba
f.getNIDA (f.all[resnum]) # improper dihedrals => f.ida
f.getNDA (f.all[resnum]) # dihedrals => f.da
# output to Gromacs format
#-------------------------#
#####
# atoms
print ""
print "[",f.residue[0],"]"
print " [ atoms ]"
chargegroup = 0
for j in range(f.natom - f.nlin):
try:
atomtype = atoi(f.atoms [j][2]) - 1
atomfield = typelines[atomtype][0]
print "%5s %5s %11s %5s" % \
(f.atoms [j][1],atomfield,f.atoms [j][4],chargegroup)
chargegroup = chargegroup + atoi(f.atoms[j][5])
except:
print j
#####
# trailing atoms
for j in range(f.nlin):
atomtype = atoi(f.atomtr [j][2]) - 1
atomfield = typelines[atomtype][0]
print "%5s %5s %11s %5s" % \
(f.atomtr[j][1],atomfield,f.atomtr[j][4][:-2],chargegroup)
chargegroup = chargegroup + atoi(f.atomtr[j][5])
#####
# bonds
print " [ bonds ]"
for j in range(f.nb):
t1 = atoi(f.bonds [j][0])
t2 = atoi(f.bonds [j][1])
" Only special bonds go to 0 or less "
if t1 >= 1 and t2 >= 1:
t1 = translate(t1)
t2 = translate(t2)
print "%5s %5s gb_%-5s" % \
(t1, t2, f.bonds[j][2])
#####
# exclusions
ne = 0
for j in range(f.natom - f.nlin):
aaa = findbonds(j)
bbb = f.atoms[j][7:]
for i in aaa:
if i in bbb: bbb.remove(i)
for i in bbb:
" Ignore special exclusions "
t1 = atoi(i)
if t1 >= 0:
t1 = translate(t1)
t2 = atoi(f.atoms[j][0])
t2 = translate(t2)
if ne == 0: print " [ exclusions ]\n; ai aj"
print "%5s %5s" % (t2,t1)
ne = ne + 1
#####
# angles
print " [ angles ]"
print "; ai aj ak gromos type"
for j in range(f.nba):
t1 = atoi(f.ba [j][0])
t2 = atoi(f.ba [j][1])
t3 = atoi(f.ba [j][2])
if t1 >= -2 and t2 >= -2 and t3 >= -2:
t1 = translate(t1)
t2 = translate(t2)
t3 = translate(t3)
print "%5s %5s %5s ga_%-5s" % \
(t1,t2,t3,f.ba[j][3])
#####
# improper dihedrals
print " [ impropers ]"
print "; ai aj ak al gromos type"
for j in range(f.nida):
t1 = atoi(f.ida [j][0])
t2 = atoi(f.ida [j][1])
t3 = atoi(f.ida [j][2])
t4 = atoi(f.ida [j][3])
if t1 >= -2 and t2 >= -2 and t3 >= -2 and t4 >= -2:
t1 = translate(t1)
t2 = translate(t2)
t3 = translate(t3)
t4 = translate(t4)
print "%5s %5s %5s %5s gi_%-5s" % \
(t1,t2,t3,t4,f.ida[j][4])
#####
# dihedrals
print " [ dihedrals ]"
print "; ai aj ak al gromos type"
for j in range(f.nda):
t1 = atoi(f.da [j][0])
t2 = atoi(f.da [j][1])
t3 = atoi(f.da [j][2])
t4 = atoi(f.da [j][3])
if t1 >= -2 and t2 >= -2 and t3 >= -2 and t4 >= -2:
t1 = translate(t1)
t2 = translate(t2)
t3 = translate(t3)
t4 = translate(t4)
print "%5s %5s %5s %5s gd_%-5s" % \
(t1,t2,t3,t4,f.da[j][4])
|
