[gmx-users] Ligand simulation

[Mark Abraham]

Hi,

On Wed, 5 Apr 2017 08:49 RAHUL SURESH <drrahulsuresh at gmail.com> wrote:

> for Command
>
>
>
> *gmx grompp -f em.mdp -c solv.gro -p conformer.top -o ions.tpr*
> I get the following error.
>
>
> *Warning: atom name 5839 in conformer.top and solv.gro does not match (H81
> - 1H8)Warning: atom name 5840 in conformer.top and solv.gro does not match
> (H82 - 2H8)*
>
> Is it really an issue or can I use -maxwarn?
>

Only you can know whether the difference in naming reflects your intent, or
not. Why did you generate the topology from a coordinate file that is
different from what you are using with grompp?

Mark

--
> *Regards,*
> *Rahul Suresh*
> *Research Scholar*
> *Bharathiar University*
> *Coimbatore*
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