[gmx-users] topology and coordinate file not matching after grompp

chinnu657 cma1g09 at soton.ac.uk
Wed Jul 31 12:04:59 CEST 2013


I have a problem and although I've read almost everything the internet could
offer on how differently people have approached this problem, mine hasn't
been solved yet.

Basically, I am trying to mix 2 different proteins in one box and after
doing my grompp to neutralise the system, I get the error number of
coordinates in coordinate file (solvated.gro, 85059) does not match topology
(topol.top, 85079). 

This is how my topology file looks:
;GROMACS toplogy

;Include the force field
#include "oplsaa.ff/forcefield.itp"

; Include chain topologies
#include "topol_1AKI.itp"
#include "topol_2CDS.itp"

;Include water topology
#include "spce.itp"

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

[ system ]
Two proteins in water

[ molecules ]
Protein_1AKI	1
Protein_2CDS	1
SOL             27053

How can I deduce from this data that the number of coordinates in topol.top
is 85079. And what exactly should I do to reduce the number of molecules
here so that the 2 files have the same number of coordinates. 

I will really appreciate the help. I am pretty new with MD simulations

Kind Regards,

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