[gmx-users] non-native contatcs

[suhani nagpal]

Hey Bipin

Thanks. yes, I  have calculated the native contacts as well as the fraction
of native contacts using the vmd extension earlier.

so, now I need to compare the two contact matrices?  ( one of native and
the other after 200ns)

as in superimpose or just by observing?

Thanks


On Wed, Jan 15, 2014 at 10:16 PM, rajat desikan <rajatdesikan at gmail.com>wrote:

> Hi,
> I have never done this before. But is this a possibility?
>
> http://www.pymolwiki.org/index.php/Contact_map_visualizer
>
>
> On Wed, Jan 15, 2014 at 8:41 PM, bipin singh <bipinelmat at gmail.com> wrote:
>
> > Hello Dr. Justin,
> >
> > Yes, there is no in-built module in Gromacs to get the information about
> > native contacts during the simulation, but I think it can be done using
> the
> > following resources outside the Gromacs:
> >
> >
> >
> http://pythonhosted.org/MDAnalysis/documentation_pages/analysis/contacts.html
> >
> > http://www.multiscalelab.org/utilities/RMSDTTNC
> >
> >
> > On Wed, Jan 15, 2014 at 7:38 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> > >
> > >
> > > On 1/15/14, 7:11 AM, bipin singh wrote:
> > >
> > >> First define and calculate the native contacts (contacts which were
> > >> present
> > >> in native reference structure and exist for significant amount of time
> > >> during simulation). Then you can identify the contacts which exist for
> > >> significant amount of time but were not present in native reference
> > >> structure (which may correspond to non-native contacts).
> > >>
> > >>
> > > Can you actually do this within Gromacs, or outside software?  I'd be
> > > curious to know.
> > >
> > > -Justin
> > >
> > >
> > >
> > >>
> > >> On Wed, Jan 15, 2014 at 1:05 PM, suhani nagpal <
> suhani.nagpal at gmail.com
> > >
> > >> wrote:
> > >>
> > >>  Greetings
> > >>>
> > >>> I'm studying protein unfolding by CTMD and REMD simulations to
> capture
> > >>> the
> > >>> intermediate states.
> > >>>
> > >>> I want to calculate the non-native contacts formed during the
> > >>> intermediate
> > >>> state.
> > >>>
> > >>>   Suggestions please
> > >>>
> > >>>
> > >>> Thanks
> > >>> Suhani
> > >>> Proteomics and Structural biology Lab
> > >>> CSIR-IGIB
> > >>> --
> > >>> 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-usersor
> > >>> send a mail to gmx-users-request at gromacs.org.
> > >>>
> > >>>
> > >>
> > >>
> > >>
> > > --
> > > ==================================================
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Postdoctoral Fellow
> > >
> > > Department of Pharmaceutical Sciences
> > > School of Pharmacy
> > > Health Sciences Facility II, Room 601
> > > University of Maryland, Baltimore
> > > 20 Penn St.
> > > Baltimore, MD 21201
> > >
> > > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > >
> > > ==================================================
> > >
> > > --
> > > 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.
> > >
> >
> >
> >
> > --
> >
> >
> >
> > *--------------------Thanks and Regards,Bipin Singh*
> > --
> > 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.
> >
>
>
>
> --
> Rajat Desikan (Ph.D Scholar)
> Prof. K. Ganapathy Ayappa's Lab (no 13),
> Dept. of Chemical Engineering,
> Indian Institute of Science, Bangalore
> --
> 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.
>