[gmx-users] Error in methanol simulation

[Justin Lemkul]

On 8/1/14, 5:09 PM, Deepak Ojha wrote:
> Dear gmx_users
> I am trying to do a simulation of methanol using the topology file from
> virtualchemistry.org.
> I created the topology file as given below
>
> ; Include forcefield parameters
> #include "methanol.itp"
>
> [ system ]
> methanol
> [ molecules ]
> methanol 108
>
> however when I do energy minimization grompp -f em.mdp -c pure.pdb -p
> test1.top -o em.tpr
> I get
>   Excluding 3 bonded neighbours molecule type 'methanol'
> Excluding 3 bonded neighbours molecule type 'methanol'
> processing coordinates...
>
> -------------------------------------------------------
> Program grompp, VERSION 4.0.7
> Source code file: ../../../../src/kernel/grompp.c, line: 362
>
> Fatal error:
> number of coordinates in coordinate file (pure.pdb, 648)
>               does not match topology (test1.top, 654)
> Any suggestions?
>

The topology specifies one more methanol molecule than the coordinates (note the 
difference is exactly 6 atoms).  Likely there is a [molecules] directive in 
methanol.itp that is specifying the additional molecule.  Kill that [molecules] 
directive and use only the one in the .top file.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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
http://mackerell.umaryland.edu/~jalemkul

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