[gmx-users] non-native contatcs

bipin singh bipinelmat at gmail.com
Mon Jan 20 15:33:35 CET 2014


>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?
In principle yes, you can get it both way i.e. by comparing the two
matrices visually or mathematically, it depends what information you are
looking for.


On Mon, Jan 20, 2014 at 5:36 PM, suhani nagpal <suhani.nagpal at gmail.com>wrote:

> 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
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> > > >>>
> > > >>>
> > > >>
> > > >>
> > > >>
> > > > --
> > > > ==================================================
> > > >
> > > > 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
> > > >
> > > > ==================================================
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> > > --
> > >
> > >
> > >
> > > *--------------------Thanks and Regards,Bipin Singh*
> > > --
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> >
> > --
> > Rajat Desikan (Ph.D Scholar)
> > Prof. K. Ganapathy Ayappa's Lab (no 13),
> > Dept. of Chemical Engineering,
> > Indian Institute of Science, Bangalore
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-- 



*--------------------Thanks and Regards,Bipin Singh*


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