[gmx-users] From: Graduate Student protein active site inquiry

[Sajeewa Pemasinghe]

Hi,

groups can be specified using

gmx select

http://biophysics.med.jhmi.edu/~yliu120/tutorials.html

and


gmx make_ndx

http://bioinf.modares.ac.ir/workshop/md_sep_03_2012/fwspidr_tutor.pdf

HTH

Sajeewa



On Sat, May 6, 2017 at 6:35 AM, Felix Y Yang <fyy001 at ucsd.edu> wrote:

> Thanks for the reply.
>
> I'm trying to test out a theory that enzymes gain "heat" from their
> substrate after the catalytic reaction finishes, thus my plan to heat up
> the active site. Is there a better approach to testing this theory?
>
> How would I specify the groups?
>
> Felix
>
>
> >
> >
> > On 5/5/17 6:56 PM, Felix Y Yang wrote:
> >> Good afternoon,
> >>
> >> I am a graduate student working at UCSD, and currently working on a few
> simple proteins like beta-amylase, insulin, and triosephosphate
> isomerase
> >> in gromacs. I'm fairly new to protein simulations in general, and I
> would
> >> like to know if there is a way to identify and isolate the active sites
> on
> >> these proteins in an index file to heat individually from the rest of
> the
> >> protein as part of a simulation I plan to do. Any feedback would be
> greatly appreciated, thank you.
> >>
> >
> > You can specify groups as tc-grps and then corresponding groups for
> simulated
> > annealing.  What you're proposing is extremely unphysical, though.
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
> > --
> > 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.
>