[gmx-users] number of coordinates in coordinate file (system_inflated.gro, 9331) number of coordinates in coordinate file does not match topology

Parul tew parultew at gmail.com
Tue Feb 15 10:25:59 CET 2011

Hi all,
first I would like to thank Justin A. Lemkul for the tutorials
provided which are very helpful for new users like me.
I am doing a membrane protein simulation and now doing packing of the
lipids around the protein. I had run the inflategro.pl script and
and now I am facing a problem doing energy minimization of my inflated
system (contatining protein and the lipid membrane) using grompp.
I have updated my topology file accordingly ie removed the spc.itp,
ions.itp it now only contains protein and dppc
the protein is of 3881 atoms but after updating my topolgy it still
gives the following error:
Fatal error:
number of coordinates in coordinate file (system_inflated.gro, 9331)
             does not match topology (topol.top, 10281)
As i understand it could be because of the deleted lipids of the
system, if so how can I know the deleted number of lipids.

My topology file looks like
;	This is your topology file
;	protein
; Include forcefield parameters
#include "ffG53a6_lipid.itp"

[ moleculetype ]
; Name            nrexcl
Protein_A           3

[ atoms ]
; Strong position restraints for InflateGRO
#include "strong_posre.itp"

; Include DPPC chain topology
#include "dppc.itp"

; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000

[ system ]
; Name
128-Lipid DPPC Bilayer

[ molecules ]
; Compound        #mols
Protein_A           1
DPPC                128

thank you,
Parul Tewatia
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