Hi Mark, <br>her is my topology,<br><br>best wishes<br>mustafa<br>;<br>; File 'topol.top' was generated<br>; By user: onbekend (0)<br>; On host: onbekend<br>; At date: Fri Jan 7 00:19:16 2011<br>;<br>; This is a standalone topology file<br>
;<br>; It was generated using program:<br>; pdb2gmx - VERSION 4.5.1<br>;<br>; Command line was:<br>; pdb2gmx -f vpgvg10.pdb -ignh <br>;<br>; Force field was read from the standard Gromacs share directory.<br>
;<br><br>; Include forcefield parameters<br>#include "gromos43a1.ff/forcefield.itp"<br><br>[ moleculetype ]<br>; Name nrexcl<br>Protein 3<br><br>[ atoms ]<br>; nr type resnr residue atom cgnr charge mass typeB chargeB massB<br>
; residue 1 VAL rtp VAL q +1.0<br> 1 NL 1 VAL N 1 0.129 14.0067 ; qtot 0.129<br> 2 H 1 VAL H1 1 0.248 1.008 ; qtot 0.377<br> 3 H 1 VAL H2 1 0.248 1.008 ; qtot 0.625<br>
4 H 1 VAL H3 1 0.248 1.008 ; qtot 0.873<br> 5 CH1 1 VAL CA 2 0.127 13.019 ; qtot 1<br> 6 CH1 1 VAL CB 2 0 13.019 ; qtot 1<br>
7 CH3 1 VAL CG1 2 0 15.035 ; qtot 1<br> 8 CH3 1 VAL CG2 2 0 15.035 ; qtot 1<br> 9 C 1 VAL C 3 0.38 12.011 ; qtot 1.38<br>
10 O 1 VAL O 3 -0.38 15.9994 ; qtot 1<br>; residue 2 PRO rtp PRO q 0.0<br> 11 N 2 PRO N 4 0 14.0067 ; qtot 1<br> 12 CH1 2 PRO CA 5 0 13.019 ; qtot 1<br>
13 CH2 2 PRO CB 5 0 14.027 ; qtot 1<br> 14 CH2 2 PRO CG 6 0 14.027 ; qtot 1<br> 15 CH2 2 PRO CD 6 0 14.027 ; qtot 1<br>
16 C 2 PRO C 7 0.38 12.011 ; qtot 1.38<br> 17 O 2 PRO O 7 -0.38 15.9994 ; qtot 1<br>; residue 3 GLY rtp GLY q 0.0<br> 18 N 3 GLY N 8 -0.28 14.0067 ; qtot 0.72<br>
19 H 3 GLY H 8 0.28 1.008 ; qtot 1<br> 20 CH2 3 GLY CA 9 0 14.027 ; qtot 1<br> 21 C 3 GLY C 10 0.38 12.011 ; qtot 1.38<br>
22 O 3 GLY O 10 -0.38 15.9994 ; qtot 1<br>; residue 4 VAL rtp VAL q 0.0<br> 23 N 4 VAL N 11 -0.28 14.0067 ; qtot 0.72<br> 24 H 4 VAL H 11 0.28 1.008 ; qtot 1<br>
25 CH1 4 VAL CA 12 0 13.019 ; qtot 1<br> 26 CH1 4 VAL CB 12 0 13.019 ; qtot 1<br> 27 CH3 4 VAL CG1 12 0 15.035 ; qtot 1<br>
28 CH3 4 VAL CG2 12 0 15.035 ; qtot 1<br> 29 C 4 VAL C 13 0.38 12.011 ; qtot 1.38<br> 30 O 4 VAL O 13 -0.38 15.9994 ; qtot 1<br>
; residue 5 GLY rtp GLY q 0.0<br> 31 N 5 GLY N 14 -0.28 14.0067 ; qtot 0.72<br> 32 H 5 GLY H 14 0.28 1.008 ; qtot 1<br> 33 CH2 5 GLY CA 15 0 14.027 ; qtot 1<br>
34 C 5 GLY C 16 0.38 12.011 ; qtot 1.38<br> 35 O 5 GLY O 16 -0.38 15.9994 ; qtot 1<br>; residue 6 VAL rtp VAL q 0.0<br> 36 N 6 VAL N 17 -0.28 14.0067 ; qtot 0.72<br>
37 H 6 VAL H 17 0.28 1.008 ; qtot 1<br> 38 CH1 6 VAL CA 18 0 13.019 ; qtot 1<br> 39 CH1 6 VAL CB 18 0 13.019 ; qtot 1<br>
40 CH3 6 VAL CG1 18 0 15.035 ; qtot 1<br> 41 CH3 6 VAL CG2 18 0 15.035 ; qtot 1<br> 42 C 6 VAL C 19 0.38 12.011 ; qtot 1.38<br>
43 O 6 VAL O 19 -0.38 15.9994 ; qtot 1<br>; residue 7 PRO rtp PRO q 0.0<br> 44 N 7 PRO N 20 0 14.0067 ; qtot 1<br> 45 CH1 7 PRO CA 21 0 13.019 ; qtot 1<br>
46 CH2 7 PRO CB 21 0 14.027 ; qtot 1<br> 47 CH2 7 PRO CG 22 0 14.027 ; qtot 1<br> 48 CH2 7 PRO CD 22 0 14.027 ; qtot 1<br>
49 C 7 PRO C 23 0.38 12.011 ; qtot 1.38<br> 50 O 7 PRO O 23 -0.38 15.9994 ; qtot 1<br>; residue 8 GLY rtp GLY q 0.0<br> 51 N 8 GLY N 24 -0.28 14.0067 ; qtot 0.72<br>
52 H 8 GLY H 24 0.28 1.008 ; qtot 1<br> 53 CH2 8 GLY CA 25 0 14.027 ; qtot 1<br> 54 C 8 GLY C 26 0.38 12.011 ; qtot 1.38<br>
55 O 8 GLY O 26 -0.38 15.9994 ; qtot 1<br>; residue 9 VAL rtp VAL q 0.0<br> 56 N 9 VAL N 27 -0.28 14.0067 ; qtot 0.72<br> 57 H 9 VAL H 27 0.28 1.008 ; qtot 1<br>
58 CH1 9 VAL CA 28 0 13.019 ; qtot 1<br> 59 CH1 9 VAL CB 28 0 13.019 ; qtot 1<br> 60 CH3 9 VAL CG1 28 0 15.035 ; qtot 1<br>
61 CH3 9 VAL CG2 28 0 15.035 ; qtot 1<br> 62 C 9 VAL C 29 0.38 12.011 ; qtot 1.38<br> 63 O 9 VAL O 29 -0.38 15.9994 ; qtot 1<br>
; residue 10 GLY rtp GLY q -1.0<br> 64 N 10 GLY N 30 -0.28 14.0067 ; qtot 0.72<br> 65 H 10 GLY H 30 0.28 1.008 ; qtot 1<br> 66 CH2 10 GLY CA 31 0 14.027 ; qtot 1<br>
67 C 10 GLY C 32 0.27 12.011 ; qtot 1.27<br> 68 OM 10 GLY O1 32 -0.635 15.9994 ; qtot 0.635<br> 69 OM 10 GLY O2 32 -0.635 15.9994 ; qtot 0<br>
<br>[ bonds ]<br>; ai aj funct c0 c1 c2 c3<br> 1 2 2 gb_2<br> 1 3 2 gb_2<br> 1 4 2 gb_2<br> 1 5 2 gb_20<br> 5 6 2 gb_26<br>
5 9 2 gb_26<br> 6 7 2 gb_26<br> 6 8 2 gb_26<br> 9 10 2 gb_4<br> 9 11 2 gb_9<br> 11 12 2 gb_20<br> 11 15 2 gb_20<br> 12 13 2 gb_26<br>
12 16 2 gb_26<br> 13 14 2 gb_26<br> 14 15 2 gb_26<br> 16 17 2 gb_4<br> 16 18 2 gb_9<br> 18 19 2 gb_2<br> 18 20 2 gb_20<br> 20 21 2 gb_26<br>
21 22 2 gb_4<br> 21 23 2 gb_9<br> 23 24 2 gb_2<br> 23 25 2 gb_20<br> 25 26 2 gb_26<br> 25 29 2 gb_26<br> 26 27 2 gb_26<br> 26 28 2 gb_26<br>
29 30 2 gb_4<br> 29 31 2 gb_9<br> 31 32 2 gb_2<br> 31 33 2 gb_20<br> 33 34 2 gb_26<br> 34 35 2 gb_4<br> 34 36 2 gb_9<br> 36 37 2 gb_2<br>
36 38 2 gb_20<br> 38 39 2 gb_26<br> 38 42 2 gb_26<br> 39 40 2 gb_26<br> 39 41 2 gb_26<br> 42 43 2 gb_4<br> 42 44 2 gb_9<br> 44 45 2 gb_20<br>
44 48 2 gb_20<br> 45 46 2 gb_26<br> 45 49 2 gb_26<br> 46 47 2 gb_26<br> 47 48 2 gb_26<br> 49 50 2 gb_4<br> 49 51 2 gb_9<br> 51 52 2 gb_2<br>
51 53 2 gb_20<br> 53 54 2 gb_26<br> 54 55 2 gb_4<br> 54 56 2 gb_9<br> 56 57 2 gb_2<br> 56 58 2 gb_20<br> 58 59 2 gb_26<br> 58 62 2 gb_26<br>
59 60 2 gb_26<br> 59 61 2 gb_26<br> 62 63 2 gb_4<br> 62 64 2 gb_9<br> 64 65 2 gb_2<br> 64 66 2 gb_20<br> 66 67 2 gb_26<br> 67 68 2 gb_5<br>
67 69 2 gb_5<br><br>[ pairs ]<br>; ai aj funct c0 c1 c2 c3<br> 1 7 1 <br> 1 8 1 <br> 1 10 1 <br> 1 11 1 <br> 2 6 1 <br>
2 9 1 <br> 3 6 1 <br> 3 9 1 <br> 4 6 1 <br> 4 9 1 <br> 5 12 1 <br> 5 15 1 <br> 6 10 1 <br> 6 11 1 <br> 7 9 1 <br> 8 9 1 <br>
9 13 1 <br> 9 14 1 <br> 9 16 1 <br> 10 12 1 <br> 10 15 1 <br> 11 17 1 <br> 11 18 1 <br> 12 19 1 <br> 12 20 1 <br> 13 17 1 <br> 13 18 1 <br>
14 16 1 <br> 15 16 1 <br> 16 21 1 <br> 17 19 1 <br> 17 20 1 <br> 18 22 1 <br> 18 23 1 <br> 19 21 1 <br> 20 24 1 <br> 20 25 1 <br> 21 26 1 <br>
21 29 1 <br> 22 24 1 <br> 22 25 1 <br> 23 27 1 <br> 23 28 1 <br> 23 30 1 <br> 23 31 1 <br> 24 26 1 <br> 24 29 1 <br> 25 32 1 <br> 25 33 1 <br>
26 30 1 <br> 26 31 1 <br> 27 29 1 <br> 28 29 1 <br> 29 34 1 <br> 30 32 1 <br> 30 33 1 <br> 31 35 1 <br> 31 36 1 <br> 32 34 1 <br> 33 37 1 <br>
33 38 1 <br> 34 39 1 <br> 34 42 1 <br> 35 37 1 <br> 35 38 1 <br> 36 40 1 <br> 36 41 1 <br> 36 43 1 <br> 36 44 1 <br> 37 39 1 <br> 37 42 1 <br>
38 45 1 <br> 38 48 1 <br> 39 43 1 <br> 39 44 1 <br> 40 42 1 <br> 41 42 1 <br> 42 46 1 <br> 42 47 1 <br> 42 49 1 <br> 43 45 1 <br> 43 48 1 <br>
44 50 1 <br> 44 51 1 <br> 45 52 1 <br> 45 53 1 <br> 46 50 1 <br> 46 51 1 <br> 47 49 1 <br> 48 49 1 <br> 49 54 1 <br> 50 52 1 <br> 50 53 1 <br>
51 55 1 <br> 51 56 1 <br> 52 54 1 <br> 53 57 1 <br> 53 58 1 <br> 54 59 1 <br> 54 62 1 <br> 55 57 1 <br> 55 58 1 <br> 56 60 1 <br> 56 61 1 <br>
56 63 1 <br> 56 64 1 <br> 57 59 1 <br> 57 62 1 <br> 58 65 1 <br> 58 66 1 <br> 59 63 1 <br> 59 64 1 <br> 60 62 1 <br> 61 62 1 <br> 62 67 1 <br>
63 65 1 <br> 63 66 1 <br> 64 68 1 <br> 64 69 1 <br> 65 67 1 <br><br>[ angles ]<br>; ai aj ak funct c0 c1 c2 c3<br> 2 1 3 2 ga_9<br>
2 1 4 2 ga_9<br> 2 1 5 2 ga_10<br> 3 1 4 2 ga_9<br> 3 1 5 2 ga_10<br> 4 1 5 2 ga_10<br> 1 5 6 2 ga_12<br> 1 5 9 2 ga_12<br>
6 5 9 2 ga_12<br> 5 6 7 2 ga_14<br> 5 6 8 2 ga_14<br> 7 6 8 2 ga_14<br> 5 9 10 2 ga_29<br> 5 9 11 2 ga_18<br> 10 9 11 2 ga_32<br>
9 11 12 2 ga_30<br> 9 11 15 2 ga_30<br> 12 11 15 2 ga_20<br> 11 12 13 2 ga_12<br> 11 12 16 2 ga_12<br> 13 12 16 2 ga_12<br> 12 13 14 2 ga_12<br>
13 14 15 2 ga_12<br> 11 15 14 2 ga_12<br> 12 16 17 2 ga_29<br> 12 16 18 2 ga_18<br> 17 16 18 2 ga_32<br> 16 18 19 2 ga_31<br> 16 18 20 2 ga_30<br>
19 18 20 2 ga_17<br> 18 20 21 2 ga_12<br> 20 21 22 2 ga_29<br> 20 21 23 2 ga_18<br> 22 21 23 2 ga_32<br> 21 23 24 2 ga_31<br> 21 23 25 2 ga_30<br>
24 23 25 2 ga_17<br> 23 25 26 2 ga_12<br> 23 25 29 2 ga_12<br> 26 25 29 2 ga_12<br> 25 26 27 2 ga_14<br> 25 26 28 2 ga_14<br> 27 26 28 2 ga_14<br>
25 29 30 2 ga_29<br> 25 29 31 2 ga_18<br> 30 29 31 2 ga_32<br> 29 31 32 2 ga_31<br> 29 31 33 2 ga_30<br> 32 31 33 2 ga_17<br> 31 33 34 2 ga_12<br>
33 34 35 2 ga_29<br> 33 34 36 2 ga_18<br> 35 34 36 2 ga_32<br> 34 36 37 2 ga_31<br> 34 36 38 2 ga_30<br> 37 36 38 2 ga_17<br> 36 38 39 2 ga_12<br>
36 38 42 2 ga_12<br> 39 38 42 2 ga_12<br> 38 39 40 2 ga_14<br> 38 39 41 2 ga_14<br> 40 39 41 2 ga_14<br> 38 42 43 2 ga_29<br> 38 42 44 2 ga_18<br>
43 42 44 2 ga_32<br> 42 44 45 2 ga_30<br> 42 44 48 2 ga_30<br> 45 44 48 2 ga_20<br> 44 45 46 2 ga_12<br> 44 45 49 2 ga_12<br> 46 45 49 2 ga_12<br>
45 46 47 2 ga_12<br> 46 47 48 2 ga_12<br> 44 48 47 2 ga_12<br> 45 49 50 2 ga_29<br> 45 49 51 2 ga_18<br> 50 49 51 2 ga_32<br> 49 51 52 2 ga_31<br>
49 51 53 2 ga_30<br> 52 51 53 2 ga_17<br> 51 53 54 2 ga_12<br> 53 54 55 2 ga_29<br> 53 54 56 2 ga_18<br> 55 54 56 2 ga_32<br> 54 56 57 2 ga_31<br>
54 56 58 2 ga_30<br> 57 56 58 2 ga_17<br> 56 58 59 2 ga_12<br> 56 58 62 2 ga_12<br> 59 58 62 2 ga_12<br> 58 59 60 2 ga_14<br> 58 59 61 2 ga_14<br>
60 59 61 2 ga_14<br> 58 62 63 2 ga_29<br> 58 62 64 2 ga_18<br> 63 62 64 2 ga_32<br> 62 64 65 2 ga_31<br> 62 64 66 2 ga_30<br> 65 64 66 2 ga_17<br>
64 66 67 2 ga_12<br> 66 67 68 2 ga_21<br> 66 67 69 2 ga_21<br> 68 67 69 2 ga_37<br><br>[ dihedrals ]<br>; ai aj ak al funct c0 c1 c2 c3 c4 c5<br>
2 1 5 9 1 gd_14<br> 1 5 6 7 1 gd_17<br> 1 5 9 11 1 gd_20<br> 5 9 11 12 1 gd_4<br> 9 11 12 16 1 gd_19<br> 12 11 15 14 1 gd_19<br>
11 12 13 14 1 gd_17<br> 11 12 16 18 1 gd_20<br> 12 13 14 15 1 gd_17<br> 13 14 15 11 1 gd_17<br> 12 16 18 20 1 gd_4<br> 16 18 20 21 1 gd_19<br>
18 20 21 23 1 gd_20<br> 20 21 23 25 1 gd_4<br> 21 23 25 29 1 gd_19<br> 23 25 26 27 1 gd_17<br> 23 25 29 31 1 gd_20<br> 25 29 31 33 1 gd_4<br>
29 31 33 34 1 gd_19<br> 31 33 34 36 1 gd_20<br> 33 34 36 38 1 gd_4<br> 34 36 38 42 1 gd_19<br> 36 38 39 40 1 gd_17<br> 36 38 42 44 1 gd_20<br>
38 42 44 45 1 gd_4<br> 42 44 45 49 1 gd_19<br> 45 44 48 47 1 gd_19<br> 44 45 46 47 1 gd_17<br> 44 45 49 51 1 gd_20<br> 45 46 47 48 1 gd_17<br>
46 47 48 44 1 gd_17<br> 45 49 51 53 1 gd_4<br> 49 51 53 54 1 gd_19<br> 51 53 54 56 1 gd_20<br> 53 54 56 58 1 gd_4<br> 54 56 58 62 1 gd_19<br>
56 58 59 60 1 gd_17<br> 56 58 62 64 1 gd_20<br> 58 62 64 66 1 gd_4<br> 62 64 66 67 1 gd_19<br> 64 66 67 69 1 gd_20<br><br>[ dihedrals ]<br>
; ai aj ak al funct c0 c1 c2 c3<br> 5 1 9 6 2 gi_2<br> 5 7 8 6 2 gi_2<br> 9 5 11 10 2 gi_1<br> 11 9 12 15 2 gi_1<br>
12 11 16 13 2 gi_2<br> 16 12 18 17 2 gi_1<br> 18 16 20 19 2 gi_1<br> 21 20 23 22 2 gi_1<br> 23 21 25 24 2 gi_1<br> 25 23 29 26 2 gi_2<br>
25 27 28 26 2 gi_2<br> 29 25 31 30 2 gi_1<br> 31 29 33 32 2 gi_1<br> 34 33 36 35 2 gi_1<br> 36 34 38 37 2 gi_1<br> 38 36 42 39 2 gi_2<br>
38 40 41 39 2 gi_2<br> 42 38 44 43 2 gi_1<br> 44 42 45 48 2 gi_1<br> 45 44 49 46 2 gi_2<br> 49 45 51 50 2 gi_1<br> 51 49 53 52 2 gi_1<br>
54 53 56 55 2 gi_1<br> 56 54 58 57 2 gi_1<br> 58 56 62 59 2 gi_2<br> 58 60 61 59 2 gi_2<br> 62 58 64 63 2 gi_1<br> 64 62 66 65 2 gi_1<br>
67 66 69 68 2 gi_1<br><br><br><br><br><br>; Include Position restraint file<br>#ifdef POSRES<br>#include "posre.itp"<br>#endif<br><br>; Include water topology<br>#include "gromos43a1.ff/methanol.itp"<br>
<br>[ system ]<br>; Name<br>Protein in methanol<br><br>[ molecules ]<br>; Compound #mols<br>Protein 1<br>MTH 660<br><br><br>Message: 7<br>
Date: Fri, 07 Jan 2011 12:41:27 +1100<br>
From: Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
Subject: Re: [gmx-users] methanol simulation error<br>
To: Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
Message-ID: <<a href="mailto:4D266F47.5000004@anu.edu.au">4D266F47.5000004@anu.edu.au</a>><br>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br>
<br>
On 7/01/2011 12:31 PM, mustafa bilsel wrote:<br>
> Hi all,<br>
> I try to make a simulation in methanol. I use gromos43a1 forcefield.<br>
> My command follow,<br>
> pdb2gmx -f xxx.pdb<br>
> editconf -f conf.gro -bt dodecahedron -d 0.8 -o box.gro<br>
> genbox -cp box.gro -cs methanol216.gro -p topol.top -o solvated.gro<br>
> When grompp for minimization it gives an error:<br>
> Atomtype CMET not found<br>
><br>
> I have used grep to count the methanol molecules and added SOL 660<br>
> comment in .top file to tell the number of methanols.<br>
> Also I added #include "gromos43a1.ff/methanol.itp" line to .top.<br>
<br>
I'm not sure why I'm repeating myself, but the name given in that<br>
moleculetype is not SOL. That name must match what appears in the<br>
[molecules] section.<br>
<br>
Please make sure you have read the examples in Chapter 5 of the manual<br>
and understand everything there.<br>
<br>
><br>
> Please don't suggest non-water solvation in how-to part of Gromacs web.<br>
><br>
> Could you tell me what missing is?<br>
<br>
You're using atomtype CMET somewhere in your .top or its #included .itp<br>
files. Your forcefield doesn't define atomtype CMET, and it needs to if<br>
your usage is correct. Without seeing your topology, we can't say more.<br>
<br>
Mark<br>
<br><br><br>