Mark:
I am sorry to disturb you. I'm a beginner of GROMACS and this "mailing-list" system. I even don't know how to replay a post directly. And yesterday I haven't seen your replay because the list title changed, sorry again!
About the problem, I haven't resolved it yet. The .top file of my ATP molecule is generated by the pdb2gmx, and the coordinates of each atom adopted to the pdb file. The force file is ffG43a2. Whether my topology file of ATP molecule have something wrong? The topology file of ATP as following:
; File '../ATP/ATP.top' was generated
; By user: root (0)
; On host: mjduan-desktop
; At date: Wed Aug 15 16:55:53 2007
;
; This is your topology file
; "Does All This Money Really Have To Go To Char ity ?" (Rick)
;
; Include forcefield parameters
#include "ffG43a2.itp"
[ moleculetype ]
; Name nrexcl
Protein 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB chargeB massB
1 NR 1 ATP AN9 1 -0.2 14.0067 ; qtot -0.2
2 C 1 60; ATP AC4 1 0.2 12.011 ; qtot 0
3 NR 1 ATP AN3 2 -0.36 14.0067 ; qtot -0.36
4 CR1 1 ATP AC2 2 0.36 13.019 ; qtot 0
5 NR 1 ATP AN1 3 -0.36 14.0067 ; qtot -0.36
6 C 1 ATP AC6 3 0.36 12.011 ; qtot 0
7 NT 1 ATP AN6 4 -0.83 14.0067 ; qtot -0.83
8 H 1 ATP AH61 4 0.415 1.008 ; qtot -0.415
9 H 1&# 160; ATP AH62 4 0.415 1.008 ; qtot 0
10 C 1 ATP AC5 5 0 12.011 ; qtot 0
11 NR 1 ATP AN7 5 -0.36 14.0067 ; qtot -0.36
12 CR1 1 ATP AC8 5 0.36 13.019&# 160; ; qtot 0
13 CH1 1 ATP AC1* 6 0.2 13.019 ; qtot 0.2
14 OA 1 ATP AO4* 6 -0.36 15.9994 ; qtot -0.16
15 CH1 1 ATP AC4* 6 0.16 13.019 ; qtot 0
16 CH1 1 ATP AC2* & #160; 7 0.15 13.019 ; qtot 0.15
17 OA 1 ATP AO2* 7 -0.548 15.9994 ; qtot -0.398
18 H 1 ATP AH2* 7 0.398 1.008 ; qtot 0
19 CH1 1 ATP AC3* 8 0.15 13.019 ; qtot 0.15
20 &# 160; OA 1 ATP AO3* 8 -0.548 15.9994 ; qtot -0.398
21 H 1 ATP AH3* 8 0.398 1.008 ; qtot 0
22 CH2 1 ATP AC5* 9 0 14.027 ; qtot 0
23 OA 1 ATP AO5* 10 -0.36 60; 15.9994 ; qtot -0.36
24 P 1 ATP APA 10 0.705 30.9738 ; qtot 0.345
25 OM 1 ATP O1PA 10 -0.635 15.9994 ; qtot -0.29
26 OM 1 ATP O2PA 10 -0.635 15.9994 ; qtot -0.925
27 OA 1 ATP O3PA &# 160; 11 -0.36 15.9994 ; qtot -1.285
28 P 1 ATP APB 11 0.705 30.9738 ; qtot -0.58
29 OM 1 ATP O1PB 11 -0.635 15.9994 ; qtot -1.215
30 OM 1 ATP O2PB 11 -0.635 15.9994 ; qtot -1.85
31 OA &# 160; 1 ATP O3PB 12 -0.36 15.9994 ; qtot -2.21
32 P 1 ATP APG 12 0.63 30.9738 ; qtot -1.58
33 OM 1 ATP O1PG 12 -0.635 15.9994 ; qtot -2.215
34 OM 1 ATP O2PG 12 -0.635 15.9994 ; qtot -2.85
; 35 OA 1 ATP O3PG 12 -0.548 15.9994 ; qtot -3.398
36 H 1 ATP H3PG 12 0.398 1.008 ; qtot -3
[ bonds ]
; ai aj funct c0 c1 c2 c3
1 2 2 gb_9
1 ; 12 2 gb_9
1 13 2 gb_21
2 3 2 gb_11
2 10 2 gb_15
3 4 2 gb_6
4 5 2 gb_6
5 6 2 gb_11
6 7 2 gb_8
6 10 2 gb_15
7 8 2 gb_2
7 ; 9 2 gb_2
10 11 2 gb_9
11 12 2 gb_9
13 14 2 gb_19
13 16 2 gb_25
14 15 2 gb_19
15 19 2 gb_25
15 22 2 gb_25
16 17 2 gb_19
16 19 2 gb_25
17 18 2 gb_1 19 20 2 gb_19
20 21 2 gb_1
22 23 2 gb_19
23 24 2 gb_27
24 25 2 gb_23
24 26 2 gb_23
24 27 2 gb_27
27 28 2 gb_27
28 29 2 gb_23
28 30 2 gb_23
28 31 2 0; gb_27
31 32 2 gb_27
32 33 2 gb_23
32 34 2 gb_23
32 35 2 gb_27
35 36 2 gb_1
[ pairs ]
; ai aj funct c0 c1 c2 c3
1 15 1
1 17 1
0; 1 19 1
2 14 1
2 16 1
5 8 1
5 9 1
7 11 1
8 10 1
9 10 1
12 14 1
12 16 1
13 18 1
13 20 1
13 22 1
14 17 0; 1
14 20 1
14 23 1
15 17 1
15 21 1
15 24 1
16 21 1
16 22 1
17 20 1
18 19 1
19 23 1
20 22 1
22 25 1
22 26 1
22 27 1
23 28 1
24 29 1
24 30 1
24 31 1
25 28 1
26 28 1
27 32 1
28 33 1
28 34 1
28 35 1
29 32 1
30 32 1
[ angles ]
; ai aj ak funct c0 c1 c2 c3
2 1 12 2 ga_6
2 1 13 2 ga_36
12 1 13 2 ga_36
1 2 3 2 ga_38
1 2 10 2 ga_6
3 2 10 2 ga_26
2 3 4 2 ga_26
3 4 5 2 ga_26
4 5 6 2 ga_26
5 6 7 2 ga_26
5 6 10 2 ga_26
7 6 10 2 ga_26
6 7 8 2 ga_22
6 7 9 2 ga_22
8 & #160; 7 9 2 ga_23
2 10 6 2 ga_26
2 10 11 2 ga_6
6 10 11 2 ga_38
10 11 12 2 ga_6
1 12 11 2 ga_6
1 13 14 2 ga_8
1 13 16 2 ga_8
14 13 16 0; 2 ga_8
13 14 15 2 ga_9
14 15 19 2 ga_8
14 15 22 2 ga_8
19 15 22 2 ga_7
13 16 17 2 ga_8
13 16 19 2 ga_7
17 16 19 2 ga_8
16 17 18 2 ga_11
15 19 16&# 160; 2 ga_7
15 19 20 2 ga_8
16 19 20 2 ga_8
19 20 21 2 ga_11
15 22 23 2 ga_8
22 23 24 2 ga_25
23 24 25 2 ga_13
23 24 26 2 ga_13
23 24 27 2 ga_4
25 24 26 2 ga_28
25 24 27 2 ga_13
26 24 27 2 ga_13
24 27 28 2 ga_25
27 28 29 2 ga_13
27 28 30 2 ga_13
27 28 31 2 ga_4
29 28 30 2 ga_28
29 28 31 2 ga_13
60; 30 28 31 2 ga_13
28 31 32 2 ga_25
31 32 33 2 ga_13
31 32 34 2 ga_13
31 32 35 2 ga_4
33 32 34 2 ga_28
33 32 35 2 ga_13
34 32 35 2 ga_13
32 35 36 2 ga_11
[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3 c4 c5
2 1 13 14 1 gd_6
10 6 7 8 1 gd_4
16 13 14 15 1 gd_14
1&# 160; 13 16 17 1 gd_7
14 13 16 17 1 gd_8
14 13 16 19 1 gd_17
14 13 16 19 1 gd_7
13 14 15 19 1 gd_14
14 15 19 16 1 gd_7
14 15 19 20 1 gd_8
22 15 19 0; 16 1 gd_17
22 15 19 20 1 gd_7
14 15 22 23 1 gd_8
19 15 22 23 1 gd_17
19 15 22 23 1 gd_7
13 16 17 18 1 gd_12
13 16 19 15 1 gd_17
13 16 19 20 1 gd_7
17 16 19 15 1 gd_7
17 16 19 20 1 gd_8
15 19 20 21 1 gd_12
15 22 23 24 1 gd_14
22 23 24 27 1 gd_11
22 23 24 27 1 gd_9
23 24 27 28 1 gd_11
23 24 27 28 1 gd_9
24 27 28 31 1 gd_11
24 27 28 31 1 gd_9
27 28 31 32 1 gd_11
27 28 31 32 1 gd_9
28 31 32 35 1 gd_11
28 31 32 35 1 gd_9
31 32 35 36 1 gd_11
31 32 35 36 1 gd_9
[ dihedrals ]
; ai aj ak al funct c0 c1 c2 c3
1 12 11 10 2 gi_1
1 2 10 11 2 gi_1
1 12 2 13 2 gi_1
60; 2 3 4 5 2 gi_1
2 10 6 5 2 gi_1
2 1 3 10 2 gi_1
2 11 6 10 2 gi_1
2 1 12 11 2 gi_1
2 10 11 12 2 gi_1
3 2 10 6 2 gi_1
3 4 5 6 2 gi_1
4 3 2 10 2 gi_1
4 5 6 10 2 gi_1
6 9 8 7 2 gi_1
6 10 5 7 2 gi_1
10 2 1 12 2 gi_1
13 1 14 ; 16 2 gi_2
13 19 17 16 2 gi_2
15 14 22 19 2 gi_2
15 20 16 19 2 gi_2
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include water topology
#include "spc.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 & #160; 1000 1000
#endif
; Include generic topology for ions
#include "ions.itp"
[ system ]
; Name
Protein in water
[ molecules ]
; Compound #mols
Protein 1
SOL 871
--------------------------------
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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
