[gmx-users] Topology file

[Justin Lemkul]

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
> topol.top!!!
> 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.

-Justin

> 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
>>
>> --
>> ==================================================
>>
>> 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
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
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-- 
==================================================

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
http://www.thelemkullab.com

==================================================