[gmx-users] Error in methanol simulation

[Deepak Ojha]

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

; Include forcefield parameters
#include "methanol.itp"

[ system ]
methanol
[ 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"