[gmx-users] Error in methanol simulation

Deepak Ojha alwaysinthemind at gmail.com
Fri Aug 1 23:09:35 CEST 2014

Dear gmx_users
I am trying to do a simulation of methanol using the topology file from
I created the topology file as given below

; Include forcefield parameters
#include "methanol.itp"

[ system ]
[ molecules ]
methanol 108

however when I do energy minimization grompp -f em.mdp -c pure.pdb -p
test1.top -o em.tpr
I get
 Excluding 3 bonded neighbours molecule type 'methanol'
Excluding 3 bonded neighbours molecule type 'methanol'
processing coordinates...

Program grompp, VERSION 4.0.7
Source code file: ../../../../src/kernel/grompp.c, line: 362

Fatal error:
number of coordinates in coordinate file (pure.pdb, 648)
             does not match topology (test1.top, 654)
Any suggestions?

DeepaK Ojha
School Of Chemistry

"Selfishness is not living as one wishes to live, it is asking others to
live as one wishes to live"

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