[gmx-users] about the topology file
Tsjerk Wassenaar
tsjerkw at gmail.com
Thu Nov 2 11:39:59 CET 2006
Hi Xiangyang Liu,
Well, it's not that part of the .top file that's problematic. Likely,
at a later point there is an "#include" directive, possibly to a file
ff***.itp, which shouldn't be #included after you define your [
moleculetype ]. Track the #include and place it at the top, before the
[ moleculetype ] directive.
Hope it helps,
Tsjerk
On 11/2/06, Xiangyang Liu <shangdongliu at gmail.com> wrote:
> hello gmx-users:
> when i enter the following :
> grompp –f em.mdp –c com_wat.gro –p com.top –o com_em.tpr
>
> "Fatal error: Invalid order for directive moleculetype, file ""com.top"",
> line 17" appeared at the end.
>
> partial content of com.top file was as following:
>
>
> ;
> ;
> ; This file was generated by PRODRG version 060825.0548
> ; PRODRG written/copyrighted by Daan van Aalten
> ; and Alexander Schuettelkopf
> ;
> ; Questions/comments to dava at davapc1.bioch.dundee.ac.uk
> ;
> ; When using this software in a publication, cite:
> ; A. W. Schuettelkopf and D. M. F. van Aalten (2004).
> ; PRODRG - a tool for high-throughput crystallography
> ; of protein-ligand complexes.
> ; Acta Crystallogr. D60, 1355--1363.
> ;
> ;
>
> [ moleculetype ]
> ; Name nrexcl
> DRG 3
>
> [ atoms ]
> ; nr type resnr resid atom cgnr charge mass
> 1 CH3 1 DRG CAH 1 0.000 15.0350
> 2 CH1 1 DRG CAS 1 0.000 13.0190
> 3 CH3 1 DRG CAT 2 0.000 15.0350
> 4 CH2 1 DRG CBI 3 0.068 14.0270
> 5 CH1 1 DRG CCF 3 0.151 13.0190
> 6 C 1 DRG CCG 3 0.466 12.0110
> 7 OS 1 DRG OCU 3 - 0.146 15.9994
> 8 O 1 DRG OBJ 3 -0.539 15.9994
> 9 N 1 DRG NCE 4 0.136 14.0067
> 10 H 1 DRG HAG 4 -0.009 1.0080
> 11 C 1 DRG CCD 4 0.390 12.0110
> 12 O 1 DRG OBH 4 -0.644 15.9994
> 13 CH1 1 DRG CCC 4 0.127 13.0190
> 14 CH2 1 DRG CBG 5 0.000 14.0270
> 15 CH1 1 DRG CAQ 5 0.000 13.0190
> 16 CH3 1 DRG CAG 6 0.000 15.0350
> 17 CH3 1 DRG CAR 7 0.017 15.0350
> 18 N 1 DRG NCB 7 0.149 14.0067
> 19 H 1 DRG HAF 7 - 0.008 1.0080
> 20 C 1 DRG CCA 7 0.428 12.0110
> 21 O 1 DRG OBF 7 -0.586 15.9994
> 22 CH1 1 DRG CBZ 8 0.115 13.0190
> 23 CH2 1 DRG CBE 8 0.051 14.0270
> 24 C 1 DRG CAO 8 0.354 12.0110
> 25 OM 1 DRG OAF 8 -0.760 15.9994
> 26 OM 1 DRG OAP 8 -0.760 15.9994
> 27 N 1 DRG NBY 9 0.035 14.0067
> 28 H 1 DRG HAE 9 -0.035 1.0080
> 29 C 1 DRG CBX 10 0.385 12.0110
> 30 O 1 DRG OBD 10 -0.651 15.9994
> 31 CH1 1 DRG CBW 10 0.125 13.0190
> 32 CH1 1 DRG CBC 10 0.126 13.0190
> 33 CH3 1 DRG CAN 10 0.015 15.0350
> 34 CH3 1 DRG CBB 11 0.000 15.0350
> 35 N 1 DRG NBV 12 0.136 14.0067
> 36 H 1 DRG HAD 12 -0.009 1.0080
> 37 C 1 DRG CBU 12 0.390 12.0110
> 38 O 1 DRG OBA 12 -0.644 15.9994
> 39 CH1 1 DRG CBT 12 0.127 13.0190
> 40 CH2 1 DRG CAZ 13 0.000 14.0270
> 41 CH1 1 DRG CAL 13 0.000 13.0190
> 42 CH3 1 DRG CAE 14 0.000 15.0350
> 43 CH3 1 DRG CAM 14 0.000 15.0350
> 44 N 1 DRG NBS 15 0.136 14.0067
> 45 H 1 DRG HAC 15 -0.009 1.0080
> 46 C 1 DRG CBR 15 0.390 12.0110
> 47 O 1 DRG OAY 15 - 0.644 15.9994
> 48 CH1 1 DRG CBQ 15 0.127 13.0190
> 49 CH2 1 DRG CAX 16 0.000 14.0270
> 50 CH1 1 DRG CAJ 16 0.000 13.0190
> 51 CH3 1 DRG CAD 17 0.000 15.0350
> 52 CH3 1 DRG CAK 17 0.000 15.0350
> 53 N 1 DRG NBP 18 0.136 14.0067
> 54 H 1 DRG HAB 18 -0.009 1.0080
> 55 C 1 DRG C 18 0.390 12.0110
> 56 O 1 DRG O 18 -0.644 15.9994
> 57 CH1 1 DRG CA 18 0.127 13.0190
> 58 CH2 1 DRG CB 19 0.000 14.0270
> 59 CH2 1 DRG CG 19 0.000 14.0270
> 60 C 1 DRG CD 20 0.363 12.0110
> 61 OM 1 DRG OE2 20 -0.740 15.9994
> 62 OM 1 DRG OE1 20 -0.740 15.9994
> 63 N 1 DRG N 20 0.127 14.0067
> 64 H 1 DRG HAA 20 -0.010 1.0080
> 65 C 1 DRG CBL 21 0.367 12.0110
> 66 O 1 DRG OAU 21 -0.684 15.9994
> 67 CH2 1 DRG CBK 21 0.053 14.0270
> 68 CS1 1 DRG CCT 21 0.211 13.0190
> 69 CH2 1 DRG CCS 21 0.053 14.0270
> 70 CH2 1 DRG CCR 22 0.000 14.0270
> 71 CH2 1 DRG CCQ 22 0.000 14.0270
> 72 CH2 1 DRG CCP 22 0.000 14.0270
> 73 CH2 1 DRG CCO 22 0.000 14.0270
> 74 CH2 1 DRG CCN 23 0.000 14.0270
> 75 CH2 1 DRG CCM 23 0.000 14.0270
> 76 CH2 1 DRG CCL 23 0.000 14.0270
> 77 CH2 1 DRG CCK 23 0.000 14.0270
> 78 CH2 1 DRG CCJ 23 0.000 14.0270
> 79 CH2 1 DRG CCI 24 0.000 14.0270
> 80 CH3 1 DRG CCH 24 0.000 15.0350
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--
Tsjerk A. Wassenaar, Ph.D.
post-doc
NMR, Utrecht University,
Padualaan 8,
3584 CH Utrecht, the Netherlands
P: +31-30-2539931
F: +31-30-2537623
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