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

[Marwa Abd El Kader]

Dear Justin,
I 've tried centering on one chain and the same problem still exists, any
suggestions?

On Fri, Feb 14, 2020, 4:01 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
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> >>
> >> jalemkul at vt.edu | (540) 231-3129
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> >>
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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
>
> ==================================================
>
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> Gromacs Users mailing list
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