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<DIV><FONT size=2>Hi,everyone,I put forward the question yesterday.</FONT></DIV>
<DIV><FONT size=2>When I run the simulation, the system always echo</FONT></DIV>
<DIV>"Fatal error: number of coordinates in coordinate file (conf.gro, 12032)
does not match topology (topol.top, 0)".</DIV>
<DIV>Mr Abraham has pointed out maybe there is something wrong with the
topol.top file.</DIV>
<DIV>Now I put the topol.top here:</DIV>
<DIV> </DIV>
<DIV><PRE>;
;        Topology file for Coarse Grained DPPC + Water
;
#include "CG.itp"
[ system ]
Coase Grained DPPC in Water
[ molecules ]
;molecule name nr.
DPPC 512
WATER 5888
</PRE><PRE><PRE>;
;        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
<PRE>Since the conf.gro file is rather large,so I will </PRE><PRE>not paste it here, and the conf.gro seems to be right.</PRE><PRE>What bothers me most is why my computer can't recognize</PRE><PRE>atom coordinates in the topol.top.Can anyone help</PRE><PRE>me out?</PRE><PRE>By the way my linux is Fedora Core5,and the Gromacs</PRE><PRE>edition is 3.3.1.</PRE></PRE></PRE></DIV></BODY></HTML>