Hi Mark,
her is my topology,
best wishes
mustafa
;
; File 'topol.top' was generated
; By user: onbekend (0)
; On host: onbekend
; At date: Fri Jan 7 00:19:16 2011
;
; This is a standalone topology file
;
; It was generated using program:
; pdb2gmx - VERSION 4.5.1
;
; Command line was:
; pdb2gmx -f vpgvg10.pdb -ignh
;
; Force field was read from the standard Gromacs share directory.
;
; Include forcefield parameters
#include "gromos43a1.ff/forcefield.itp"
[ moleculetype ]
; Name nrexcl
Protein 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
typeB chargeB massB
; residue 1 VAL rtp VAL q +1.0
1 NL 1 VAL N 1 0.129 14.0067 ; qtot
0.129
2 H 1 VAL H1 1 0.248 1.008 ; qtot
0.377
3 H 1 VAL H2 1 0.248 1.008 ; qtot
0.625
4 H 1 VAL H3 1 0.248 1.008 ; qtot
0.873
5 CH1 1 VAL CA 2 0.127 13.019 ; qtot
1
6 CH1 1 VAL CB 2 0 13.019 ; qtot
1
7 CH3 1 VAL CG1 2 0 15.035 ; qtot
1
8 CH3 1 VAL CG2 2 0 15.035 ; qtot
1
9 C 1 VAL C 3 0.38 12.011 ; qtot
1.38
10 O 1 VAL O 3 -0.38 15.9994 ; qtot
1
; residue 2 PRO rtp PRO q 0.0
11 N 2 PRO N 4 0 14.0067 ; qtot
1
12 CH1 2 PRO CA 5 0 13.019 ; qtot
1
13 CH2 2 PRO CB 5 0 14.027 ; qtot
1
14 CH2 2 PRO CG 6 0 14.027 ; qtot
1
15 CH2 2 PRO CD 6 0 14.027 ; qtot
1
16 C 2 PRO C 7 0.38 12.011 ; qtot
1.38
17 O 2 PRO O 7 -0.38 15.9994 ; qtot
1
; residue 3 GLY rtp GLY q 0.0
18 N 3 GLY N 8 -0.28 14.0067 ; qtot
0.72
19 H 3 GLY H 8 0.28 1.008 ; qtot
1
20 CH2 3 GLY CA 9 0 14.027 ; qtot
1
21 C 3 GLY C 10 0.38 12.011 ; qtot
1.38
22 O 3 GLY O 10 -0.38 15.9994 ; qtot
1
; residue 4 VAL rtp VAL q 0.0
23 N 4 VAL N 11 -0.28 14.0067 ; qtot
0.72
24 H 4 VAL H 11 0.28 1.008 ; qtot
1
25 CH1 4 VAL CA 12 0 13.019 ; qtot
1
26 CH1 4 VAL CB 12 0 13.019 ; qtot
1
27 CH3 4 VAL CG1 12 0 15.035 ; qtot
1
28 CH3 4 VAL CG2 12 0 15.035 ; qtot
1
29 C 4 VAL C 13 0.38 12.011 ; qtot
1.38
30 O 4 VAL O 13 -0.38 15.9994 ; qtot
1
; residue 5 GLY rtp GLY q 0.0
31 N 5 GLY N 14 -0.28 14.0067 ; qtot
0.72
32 H 5 GLY H 14 0.28 1.008 ; qtot
1
33 CH2 5 GLY CA 15 0 14.027 ; qtot
1
34 C 5 GLY C 16 0.38 12.011 ; qtot
1.38
35 O 5 GLY O 16 -0.38 15.9994 ; qtot
1
; residue 6 VAL rtp VAL q 0.0
36 N 6 VAL N 17 -0.28 14.0067 ; qtot
0.72
37 H 6 VAL H 17 0.28 1.008 ; qtot
1
38 CH1 6 VAL CA 18 0 13.019 ; qtot
1
39 CH1 6 VAL CB 18 0 13.019 ; qtot
1
40 CH3 6 VAL CG1 18 0 15.035 ; qtot
1
41 CH3 6 VAL CG2 18 0 15.035 ; qtot
1
42 C 6 VAL C 19 0.38 12.011 ; qtot
1.38
43 O 6 VAL O 19 -0.38 15.9994 ; qtot
1
; residue 7 PRO rtp PRO q 0.0
44 N 7 PRO N 20 0 14.0067 ; qtot
1
45 CH1 7 PRO CA 21 0 13.019 ; qtot
1
46 CH2 7 PRO CB 21 0 14.027 ; qtot
1
47 CH2 7 PRO CG 22 0 14.027 ; qtot
1
48 CH2 7 PRO CD 22 0 14.027 ; qtot
1
49 C 7 PRO C 23 0.38 12.011 ; qtot
1.38
50 O 7 PRO O 23 -0.38 15.9994 ; qtot
1
; residue 8 GLY rtp GLY q 0.0
51 N 8 GLY N 24 -0.28 14.0067 ; qtot
0.72
52 H 8 GLY H 24 0.28 1.008 ; qtot
1
53 CH2 8 GLY CA 25 0 14.027 ; qtot
1
54 C 8 GLY C 26 0.38 12.011 ; qtot
1.38
55 O 8 GLY O 26 -0.38 15.9994 ; qtot
1
; residue 9 VAL rtp VAL q 0.0
56 N 9 VAL N 27 -0.28 14.0067 ; qtot
0.72
57 H 9 VAL H 27 0.28 1.008 ; qtot
1
58 CH1 9 VAL CA 28 0 13.019 ; qtot
1
59 CH1 9 VAL CB 28 0 13.019 ; qtot
1
60 CH3 9 VAL CG1 28 0 15.035 ; qtot
1
61 CH3 9 VAL CG2 28 0 15.035 ; qtot
1
62 C 9 VAL C 29 0.38 12.011 ; qtot
1.38
63 O 9 VAL O 29 -0.38 15.9994 ; qtot
1
; residue 10 GLY rtp GLY q -1.0
64 N 10 GLY N 30 -0.28 14.0067 ; qtot
0.72
65 H 10 GLY H 30 0.28 1.008 ; qtot
1
66 CH2 10 GLY CA 31 0 14.027 ; qtot
1
67 C 10 GLY C 32 0.27 12.011 ; qtot
1.27
68 OM 10 GLY O1 32 -0.635 15.9994 ; qtot
0.635
69 OM 10 GLY O2 32 -0.635 15.9994 ; qtot
0
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 2 gb_2
1 3 2 gb_2
1 4 2 gb_2
1 5 2 gb_20
5 6 2 gb_26
5 9 2 gb_26
6 7 2 gb_26
6 8 2 gb_26
9 10 2 gb_4
9 11 2 gb_9
11 12 2 gb_20
11 15 2 gb_20
12 13 2 gb_26
12 16 2 gb_26
13 14 2 gb_26
14 15 2 gb_26
16 17 2 gb_4
16 18 2 gb_9
18 19 2 gb_2
18 20 2 gb_20
20 21 2 gb_26
21 22 2 gb_4
21 23 2 gb_9
23 24 2 gb_2
23 25 2 gb_20
25 26 2 gb_26
25 29 2 gb_26
26 27 2 gb_26
26 28 2 gb_26
29 30 2 gb_4
29 31 2 gb_9
31 32 2 gb_2
31 33 2 gb_20
33 34 2 gb_26
34 35 2 gb_4
34 36 2 gb_9
36 37 2 gb_2
36 38 2 gb_20
38 39 2 gb_26
38 42 2 gb_26
39 40 2 gb_26
39 41 2 gb_26
42 43 2 gb_4
42 44 2 gb_9
44 45 2 gb_20
44 48 2 gb_20
45 46 2 gb_26
45 49 2 gb_26
46 47 2 gb_26
47 48 2 gb_26
49 50 2 gb_4
49 51 2 gb_9
51 52 2 gb_2
51 53 2 gb_20
53 54 2 gb_26
54 55 2 gb_4
54 56 2 gb_9
56 57 2 gb_2
56 58 2 gb_20
58 59 2 gb_26
58 62 2 gb_26
59 60 2 gb_26
59 61 2 gb_26
62 63 2 gb_4
62 64 2 gb_9
64 65 2 gb_2
64 66 2 gb_20
66 67 2 gb_26
67 68 2 gb_5
67 69 2 gb_5
[ pairs ]
; ai aj funct c0 c1 c2 c3
1 7 1
1 8 1
1 10 1
1 11 1
2 6 1
2 9 1
3 6 1
3 9 1
4 6 1
4 9 1
5 12 1
5 15 1
6 10 1
6 11 1
7 9 1
8 9 1
9 13 1
9 14 1
9 16 1
10 12 1
10 15 1
11 17 1
11 18 1
12 19 1
12 20 1
13 17 1
13 18 1
14 16 1
15 16 1
16 21 1
17 19 1
17 20 1
18 22 1
18 23 1
19 21 1
20 24 1
20 25 1
21 26 1
21 29 1
22 24 1
22 25 1
23 27 1
23 28 1
23 30 1
23 31 1
24 26 1
24 29 1
25 32 1
25 33 1
26 30 1
26 31 1
27 29 1
28 29 1
29 34 1
30 32 1
30 33 1
31 35 1
31 36 1
32 34 1
33 37 1
33 38 1
34 39 1
34 42 1
35 37 1
35 38 1
36 40 1
36 41 1
36 43 1
36 44 1
37 39 1
37 42 1
38 45 1
38 48 1
39 43 1
39 44 1
40 42 1
41 42 1
42 46 1
42 47 1
42 49 1
43 45 1
43 48 1
44 50 1
44 51 1
45 52 1
45 53 1
46 50 1
46 51 1
47 49 1
48 49 1
49 54 1
50 52 1
50 53 1
51 55 1
51 56 1
52 54 1
53 57 1
53 58 1
54 59 1
54 62 1
55 57 1
55 58 1
56 60 1
56 61 1
56 63 1
56 64 1
57 59 1
57 62 1
58 65 1
58 66 1
59 63 1
59 64 1
60 62 1
61 62 1
62 67 1
63 65 1
63 66 1
64 68 1
64 69 1
65 67 1
[ angles ]
; ai aj ak funct c0 c1 c2
c3
2 1 3 2 ga_9
2 1 4 2 ga_9
2 1 5 2 ga_10
3 1 4 2 ga_9
3 1 5 2 ga_10
4 1 5 2 ga_10
1 5 6 2 ga_12
1 5 9 2 ga_12
6 5 9 2 ga_12
5 6 7 2 ga_14
5 6 8 2 ga_14
7 6 8 2 ga_14
5 9 10 2 ga_29
5 9 11 2 ga_18
10 9 11 2 ga_32
9 11 12 2 ga_30
9 11 15 2 ga_30
12 11 15 2 ga_20
11 12 13 2 ga_12
11 12 16 2 ga_12
13 12 16 2 ga_12
12 13 14 2 ga_12
13 14 15 2 ga_12
11 15 14 2 ga_12
12 16 17 2 ga_29
12 16 18 2 ga_18
17 16 18 2 ga_32
16 18 19 2 ga_31
16 18 20 2 ga_30
19 18 20 2 ga_17
18 20 21 2 ga_12
20 21 22 2 ga_29
20 21 23 2 ga_18
22 21 23 2 ga_32
21 23 24 2 ga_31
21 23 25 2 ga_30
24 23 25 2 ga_17
23 25 26 2 ga_12
23 25 29 2 ga_12
26 25 29 2 ga_12
25 26 27 2 ga_14
25 26 28 2 ga_14
27 26 28 2 ga_14
25 29 30 2 ga_29
25 29 31 2 ga_18
30 29 31 2 ga_32
29 31 32 2 ga_31
29 31 33 2 ga_30
32 31 33 2 ga_17
31 33 34 2 ga_12
33 34 35 2 ga_29
33 34 36 2 ga_18
35 34 36 2 ga_32
34 36 37 2 ga_31
34 36 38 2 ga_30
37 36 38 2 ga_17
36 38 39 2 ga_12
36 38 42 2 ga_12
39 38 42 2 ga_12
38 39 40 2 ga_14
38 39 41 2 ga_14
40 39 41 2 ga_14
38 42 43 2 ga_29
38 42 44 2 ga_18
43 42 44 2 ga_32
42 44 45 2 ga_30
42 44 48 2 ga_30
45 44 48 2 ga_20
44 45 46 2 ga_12
44 45 49 2 ga_12
46 45 49 2 ga_12
45 46 47 2 ga_12
46 47 48 2 ga_12
44 48 47 2 ga_12
45 49 50 2 ga_29
45 49 51 2 ga_18
50 49 51 2 ga_32
49 51 52 2 ga_31
49 51 53 2 ga_30
52 51 53 2 ga_17
51 53 54 2 ga_12
53 54 55 2 ga_29
53 54 56 2 ga_18
55 54 56 2 ga_32
54 56 57 2 ga_31
54 56 58 2 ga_30
57 56 58 2 ga_17
56 58 59 2 ga_12
56 58 62 2 ga_12
59 58 62 2 ga_12
58 59 60 2 ga_14
58 59 61 2 ga_14
60 59 61 2 ga_14
58 62 63 2 ga_29
58 62 64 2 ga_18
63 62 64 2 ga_32
62 64 65 2 ga_31
62 64 66 2 ga_30
65 64 66 2 ga_17
64 66 67 2 ga_12
66 67 68 2 ga_21
66 67 69 2 ga_21
68 67 69 2 ga_37
[ dihedrals ]
; ai aj ak al funct c0 c1
c2 c3 c4 c5
2 1 5 9 1 gd_14
1 5 6 7 1 gd_17
1 5 9 11 1 gd_20
5 9 11 12 1 gd_4
9 11 12 16 1 gd_19
12 11 15 14 1 gd_19
11 12 13 14 1 gd_17
11 12 16 18 1 gd_20
12 13 14 15 1 gd_17
13 14 15 11 1 gd_17
12 16 18 20 1 gd_4
16 18 20 21 1 gd_19
18 20 21 23 1 gd_20
20 21 23 25 1 gd_4
21 23 25 29 1 gd_19
23 25 26 27 1 gd_17
23 25 29 31 1 gd_20
25 29 31 33 1 gd_4
29 31 33 34 1 gd_19
31 33 34 36 1 gd_20
33 34 36 38 1 gd_4
34 36 38 42 1 gd_19
36 38 39 40 1 gd_17
36 38 42 44 1 gd_20
38 42 44 45 1 gd_4
42 44 45 49 1 gd_19
45 44 48 47 1 gd_19
44 45 46 47 1 gd_17
44 45 49 51 1 gd_20
45 46 47 48 1 gd_17
46 47 48 44 1 gd_17
45 49 51 53 1 gd_4
49 51 53 54 1 gd_19
51 53 54 56 1 gd_20
53 54 56 58 1 gd_4
54 56 58 62 1 gd_19
56 58 59 60 1 gd_17
56 58 62 64 1 gd_20
58 62 64 66 1 gd_4
62 64 66 67 1 gd_19
64 66 67 69 1 gd_20
[ dihedrals ]
; ai aj ak al funct c0 c1
c2 c3
5 1 9 6 2 gi_2
5 7 8 6 2 gi_2
9 5 11 10 2 gi_1
11 9 12 15 2 gi_1
12 11 16 13 2 gi_2
16 12 18 17 2 gi_1
18 16 20 19 2 gi_1
21 20 23 22 2 gi_1
23 21 25 24 2 gi_1
25 23 29 26 2 gi_2
25 27 28 26 2 gi_2
29 25 31 30 2 gi_1
31 29 33 32 2 gi_1
34 33 36 35 2 gi_1
36 34 38 37 2 gi_1
38 36 42 39 2 gi_2
38 40 41 39 2 gi_2
42 38 44 43 2 gi_1
44 42 45 48 2 gi_1
45 44 49 46 2 gi_2
49 45 51 50 2 gi_1
51 49 53 52 2 gi_1
54 53 56 55 2 gi_1
56 54 58 57 2 gi_1
58 56 62 59 2 gi_2
58 60 61 59 2 gi_2
62 58 64 63 2 gi_1
64 62 66 65 2 gi_1
67 66 69 68 2 gi_1
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include water topology
#include "gromos43a1.ff/methanol.itp"
[ system ]
; Name
Protein in methanol
[ molecules ]
; Compound #mols
Protein 1
MTH 660
Message: 7
Date: Fri, 07 Jan 2011 12:41:27 +1100
From: Mark Abraham <mark.abra...@anu.edu.au>
Subject: Re: [gmx-users] methanol simulation error
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <4d266f47.5000...@anu.edu.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 7/01/2011 12:31 PM, mustafa bilsel wrote:
> Hi all,
> I try to make a simulation in methanol. I use gromos43a1 forcefield.
> My command follow,
> pdb2gmx -f xxx.pdb
> editconf -f conf.gro -bt dodecahedron -d 0.8 -o box.gro
> genbox -cp box.gro -cs methanol216.gro -p topol.top -o solvated.gro
> When grompp for minimization it gives an error:
> Atomtype CMET not found
>
> I have used grep to count the methanol molecules and added SOL 660
> comment in .top file to tell the number of methanols.
> Also I added #include "gromos43a1.ff/methanol.itp" line to .top.
I'm not sure why I'm repeating myself, but the name given in that
moleculetype is not SOL. That name must match what appears in the
[molecules] section.
Please make sure you have read the examples in Chapter 5 of the manual
and understand everything there.
>
> Please don't suggest non-water solvation in how-to part of Gromacs web.
>
> Could you tell me what missing is?
You're using atomtype CMET somewhere in your .top or its #included .itp
files. Your forcefield doesn't define atomtype CMET, and it needs to if
your usage is correct. Without seeing your topology, we can't say more.
Mark
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