[gmx-users] Error in methanol simulation

[Dr. Vitaly Chaban]

One MeOH molecule has run away from your PDB file.

Maybe something wrong with formatting?


Dr. Vitaly V. Chaban

Виталий Витальевич ЧАБАН




On Sat, Aug 2, 2014 at 12:09 AM, Deepak Ojha <alwaysinthemind at gmail.com> 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?
>
> --
> DeepaK Ojha
> School Of Chemistry
>
> "Selfishness is not living as one wishes to live, it is asking others to
> live as one wishes to live"
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