[gmx-users] coarse grain topology file
Shanshan Qin
sansanqin00 at mails.tsinghua.edu.cn
Sat Mar 24 14:30:19 CET 2007
Hi,everyone,I put forward the question yesterday.
When I run the simulation, the system always echo
"Fatal error: number of coordinates in coordinate file (conf.gro, 12032) does not match topology (topol.top, 0)".
Mr Abraham has pointed out maybe there is something wrong with the topol.top file.
Now I put the topol.top here:
;
; Topology file for Coarse Grained DPPC + Water
;
#include "CG.itp"
[ system ]
Coase Grained DPPC in Water
[ molecules ]
;molecule name nr.
DPPC 512
WATER 5888
;
; CG.itp: force field file for
; Coarse Grained DPPC and Water
;
[ defaults ]
1 1
[ atomtypes ]
; type mass charge ptype c6 c12
; polar type
P 72.0 0.000 A 0.0 0.0
; non polar
Na 72.0 0.000 A 0.0 0.0
; apolar
C 72.0 0.000 A 0.0 0.0
; charged
Q0 72.0 0.000 A 0.0 0.0
Qa 72.0 0.000 A 0.0 0.0
[ nonbond_params ]
; i j fund c6 c12
P P 1 0.21558E-00 0.23238E-02
Na Na 1 0.18108E-00 0.19520E-02
C C 1 0.14660E-00 0.15802E-02
Q0 Q0 1 0.14660E-00 0.15802E-02
Qa Qa 1 0.14660E-00 0.15802E-02
P Na 1 0.14660E-00 0.15802E-02
P C 1 0.77610E-01 0.83658E-03
P Q0 1 0.21558E-00 0.23238E-02
P Qa 1 0.21558E-00 0.23238E-02
Na C 1 0.11210E-00 0.12084E-02
Na Q0 1 0.14660E-00 0.15802E-02
Na Qa 1 0.14660E-00 0.15802E-02
C Q0 1 0.77610E-01 0.83658E-03
C Qa 1 0.77610E-01 0.83658E-03
Q0 Qa 1 0.14660E-00 0.15802E-02
;; Coarse Grained Water Molecule
[ moleculetype ]
; name nrexcl
WATER 2
[ atoms ]
; nr type resnr residu atom cgnr charge mass
1 P 1 WATER W 1 0 72.000
;; Coarse Grained DPPC Molecule
[ moleculetype ]
; name nrexxl
DPPC 1
[ atoms ]
; nr type resnr residu atom cgnr charge mass
1 Q0 1 DPPC NC3 1 1.0 72.000
2 Qa 1 DPPC PO4 2 -1.0 72.000
3 Na 1 DPPC GL1 3 0 72.000
4 Na 1 DPPC GL2 4 0 72.000
5 C 1 DPPC C1A 5 0 72.000
6 C 1 DPPC C2A 6 0 72.000
7 C 1 DPPC C3A 7 0 72.000
8 C 1 DPPC C4A 8 0 72.000
9 C 1 DPPC C1B 9 0 72.000
10 C 1 DPPC C2B 10 0 72.000
11 C 1 DPPC C3B 11 0 72.000
12 C 1 DPPC C4B 12 0 72.000
[ bonds ]
; ai aj funct length force.c
1 2 1 0.470 1250
2 3 1 0.470 1250
3 4 1 0.470 1250
3 5 1 0.470 1250
5 6 1 0.470 1250
6 7 1 0.470 1250
7 8 1 0.470 1250
4 9 1 0.470 1250
9 10 1 0.470 1250
10 11 1 0.470 1250
11 12 1 0.470 1250
[ angles ]
; i j k funct angle force.c
2 3 4 2 120.000 25.0
2 3 5 2 180.000 25.0
3 5 6 2 180.000 25.0
5 6 7 2 180.000 25.0
6 7 8 2 180.000 25.0
4 9 10 2 180.000 25.0
9 10 11 2 180.000 25.0
10 11 12 2 180.000 25.0
Since the conf.gro file is rather large,so I will not paste it here, and the conf.gro seems to be right.What bothers me most is why my computer can't recognizeatom coordinates in the topol.top.Can anyone helpme out?By the way my linux is Fedora Core5,and the Gromacsedition is 3.3.1.
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