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

[Justin Lemkul]

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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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