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

2013-07-31 Thread chinnu657 
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_1AKI1
Protein_2CDS1
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,
Chinnu



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

2013-07-31 Thread 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_1AKI1
Protein_2CDS1
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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