[gmx-users] non-native contatcs

[rajat desikan]

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
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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