[gmx-users] Topology file
jalemkul at vt.edu
Thu Oct 18 01:50:27 CEST 2018
On 10/17/18 6:25 PM, Mahdi Sobati Nezhad wrote:
> thanks Justin for your helps.
> the pdb2gmx make posre_chain_A.itp but don't write any thing about it in my
> Can I add it in my topol.top file?! And what's its template for it?!
If pdb2gmx completed successfully, it's there. Check again.
> 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
>>> no any porse.itp
>>> What can I do?!
>>> Do it's important that porse.itp should be in topol.top or its enough
>>> 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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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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