[gmx-users] Trajectory optimization - 2 chains are separated

[Justin Lemkul]

On 2/14/20 2:48 AM, Marwa Abd El Kader wrote:
> Dear Justin,
> Would you please tell me how, give me an example code, because I'm a novice?

The same thing you did before but instead of trying to select 
interfacial residues, make an index group of one of the protein chains 
and select it for the centering group.

-Justin

> Thanks in advance,
> Marwa
>
> On Fri, Feb 14, 2020, 4:33 AM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> On 2/13/20 1:33 PM, Marwa Abd El Kader wrote:
>>> Dear gmx-users mailing list team,
>>> I want to know how to fix the separation of 2 chains after the production
>>> run. I'm trying different combinations of trjconv after creating an index
>>> file having a specific residue(s) on the interface between the 2 chains,
>>> but nothing is working. I fixed this issue before but when there was only
>>> one chain, now with 2 chains, I don't know how to rejoin them together
>>> again. Can you suggest me any solution, please?!
>>> *N.B: the 2 chains are considered as one when selected in VMD
>> Center on a single chain rather than trying to work with the interface
>> residues.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Office: 301 Fralin Hall
>> Lab: 303 Engel Hall
>>
>> Virginia Tech Department of Biochemistry
>> 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
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

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

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