[gmx-users] grompp error no. of coordinate file doesn't match with topology file

nitu sharma sharmanitu35 at gmail.com
Thu Apr 16 11:59:32 CEST 2009

Dear all

                 I am doing simulation of membrane protein ,for this first i
did the  concatanation of protein in lipid bilayer in proper orientation
after that  I am using inflategro script of teleman sir
but after doing first step successfully I am getting problem in second step
i,e energy minimisation step.
problem is related with coordinate file which I putted with grompp and my
topology file which I have made like this-

Include forcefield parameters
#include "ffG53a6_lipid.itp"

; Include DMPC chain topology
#include "dmpc.itp"

; Include protein chain topologies
#include "tap-mod.itp"

#include "tap-mod_pr.itp"

; Include generic topology for ions
#include "ions.itp"

[ system ]
; Name
Protein in DMPC bilayer

[ molecules ]
; Name            number
Protein_X          1
DMPC              119
NA+               1

And the problem I am getting like this--
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.12#
checking input for internal consistency...
processing topology...
Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp
Generated 770 of the 2278 non-bonded parameter combinations
Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp
Excluding 3 bonded neighbours molecule type 'Protein_X'
Excluding 3 bonded neighbours molecule type 'DMPC'
Excluding 1 bonded neighbours molecule type 'NA+'
processing coordinates...

Program grompp, VERSION 4.0.3
Source code file: grompp.c, line: 362

Fatal error:
number of coordinates in coordinate file (inflated_dmpc.gro, 13253)
             does not match topology (inflated_dmpc.top, 15392)

If anyone have idea about this problem please suggest me something to solve
this problem.

Thnks a lot in advance.

Nitu Sharma
School of life sciences.
Jawaherlal Nehru University
New Delhi , India
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