[gmx-users] Topology file

[Justin Lemkul]

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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340 West Campus Dr.
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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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