On 7/31/13 6:04 AM, chinnu657 wrote:
Hello,
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.
Number of atoms in Protein_1AKI [moleculetype] + number of atoms in Protein_2CDS
[moleculetype] + (3*27053) is the number of atoms that the topology specifies.
Cross-check that against the coordinate file. This error always arises for the
same reason - incorrect bookkeeping of some sort. You haven't said how you
built the system or what commands you gave, for instance, to genbox, so it's
hard to be more specific.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
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