[gmx-users] Topology file
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.
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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