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

[Dallas Warren]

Provide the command lines and images showing what is happening, that might
help provide some insight for those trying to help.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Sun, 16 Feb 2020 at 01:52, Marwa Abd El Kader <
ph.marwaabdelkader at gmail.com> wrote:

> 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
> > >> 340 West Campus Dr.
> > >> Blacksburg, VA 24061
> > >>
> > >> jalemkul at vt.edu | (540) 231-3129
> > >> http://www.thelemkullab.com
> > >>
> > >> ==================================================
> > >>
> > >> --
> > >> Gromacs Users mailing list
> > >>
> > >> * Please search the archive at
> > >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > >> posting!
> > >>
> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >>
> > >> * For (un)subscribe requests visit
> > >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > >> send a mail to gmx-users-request at gromacs.org.
> > >>
> >
> > --
> > ==================================================
> >
> > 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
> >
> > ==================================================
> >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>