[gmx-users] Topology file

[Mahdi Sobati Nezhad]

thanks Justin for your helps.
the pdb2gmx make posre_chain_A.itp but don't write any thing about it in my
topol.top!!!
Can I add it in my topol.top file?! And what's its template for it?!

On Fri, 5 Oct 2018 17:08 Justin Lemkul, <jalemkul at vt.edu> wrote:

>
>
> On 10/4/18 6:53 PM, Mahdi Sobati Nezhad wrote:
> > Hello Gromacs users.
> > When I use pdb2gmx the Gromacs make pores.itp but in my topol.top there
> is
> > no any porse.itp
> > What can I do?!
> > Do it's important that porse.itp should be in topol.top or its enough
> that
> > pdb2gmx make porse.itp?!
>
> pdb2gmx writes the restraint file by default and it is a non-optional
> output. If you didn't get a posre.itp file, there should be glaringly
> obvious error messages as to why pdb2gmx failed. If pdb2gmx completed
> normally, you must have a restraint file. It may be named something
> different (like posre_Chain_A.itp or something) if you have chain
> identifiers in your input coordinate file.
>
> -Justin
>
> --
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>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
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