[gmx-users] problem regarding .top file generated by genbox
sudheer babu
sudheer.pbm07 at gmail.com
Mon Feb 18 15:58:22 CET 2008
HI gmxusers,
i am using gromacs version 3.3.1
i am new to gromocs, i was taken protein.top file (which is generated by
pdb2gmx). In this file i have included ff.itp , popc.itp and lipid.itp but
protein atom types already there (generated by pdb2gmx). This .top file used
for inserting of protein into mebranes by using genbox. It was run without
problem, given .gro which contain both protein and popc and .top file . when
i have used this .top and .gro for energy minimisation it's showing that,
Fatal error:
Atom types NR, HC , CR1 not found
these type of atoms not there in .gro file but present in .top file .
Iam pasting the aminoacids which contain these type of atoms
17 N 3 HISH N 7 -0.28 14.0067 ; qtot
0.72
18 H 3 HISH H 7 0.28 1.008 ; qtot
1
19 CH1 3 HISH CA 8 0 13.019 ; qtot
1
20 CH2 3 HISH CB 8 0 14.027 ; qtot
1
21 C 3 HISH CG 9 -0.05 12.011 ; qtot
0.95
22 NR 3 HISH ND1 9 0.38 14.0067 ; qtot
1.33
23 H 3 HISH HD1 9 0.3 1.008 ; qtot
1.63
24 CR1 3 HISH CD2 9 0 13.019 ; qtot
1.63
25 CR1 3 HISH CE1 9 -0.24 13.019 ; qtot
1.39
26 NR 3 HISH NE2 9 0.31 14.0067 ; qtot
1.7
27 H 3 HISH HE2 9 0.3 1.008 ; qtot
2
28 C 3 HISH C 10 0.38 12.011 ; qtot
2.38
29 O 3 HISH O 10 -0.38 15.9994 ; qtot
2
30 N 4 HISH N 11 -0.28 14.0067 ; qtot
1.72
31 H 4 HISH H 11 0.28 1.008 ; qtot
2
32 CH1 4 HISH CA 12 0 13.019 ; qtot
2
33 CH2 4 HISH CB 12 0 14.027 ; qtot
2
34 C 4 HISH CG 13 -0.05 12.011 ; qtot
1.95
35 NR 4 HISH ND1 13 0.38 14.0067 ; qtot
2.33
36 H 4 HISH HD1 13 0.3 1.008 ; qtot
2.63
37 CR1 4 HISH CD2 13 0 13.019 ; qtot
2.63
38 CR1 4 HISH CE1 13 -0.24 13.019 ; qtot
2.39
39 NR 4 HISH NE2 13 0.31 14.0067 ; qtot
2.7
40 H 4 HISH HE2 13 0.3 1.008 ; qtot
3
41 C 4 HISH C 14 0.38 12.011 ; qtot
3.38
42 O 4 HISH O 14 -0.38 15.9994 ; qtot
3
308 N 36 PHE N 133 -0.28 14.0067 ; qtot
2.72
309 H 36 PHE H 133 0.28 1.008 ; qtot
3
310 CH1 36 PHE CA 134 0 13.019 ; qtot
3
311 CH2 36 PHE CB 134 0 14.027 ; qtot
3
312 C 36 PHE CG 134 0 12.011 ; qtot
3
313 C 36 PHE CD1 135 -0.1 12.011 ; qtot
2.9
314 HC 36 PHE HD1 135 0.1 1.008 ; qtot
3
315 C 36 PHE CD2 136 -0.1 12.011 ; qtot
2.9
316 HC 36 PHE HD2 136 0.1 1.008 ; qtot
3
317 C 36 PHE CE1 137 -0.1 12.011 ; qtot
2.9
318 HC 36 PHE HE1 137 0.1 1.008 ; qtot
3
319 C 36 PHE CE2 138 -0.1 12.011 ; qtot
2.9
320 HC 36 PHE HE2 138 0.1 1.008 ; qtot
3
321 C 36 PHE CZ 139 -0.1 12.011 ; qtot
2.9
322 HC 36 PHE HZ 139 0.1 1.008 ; qtot
3
323 C 36 PHE C 140 0.38 12.011 ; qtot
3.38
324 O 36 PHE O 140 -0.38 15.9994 ; qtot
3
have i given wrong command
pls help me,
thanks in advance.
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