[gmx-users] Topology file

Justin Lemkul jalemkul at vt.edu
Fri Oct 5 15:37:43 CEST 2018

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 A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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