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 <[EMAIL PROTECTED]> 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 [EMAIL PROTECTED]
;
; 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
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read
http://www.gromacs.org/mailing_lists/users.php
--
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
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
