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

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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