[gmx-users] non-native contatcs

bipin singh bipinelmat at gmail.com
Mon Jan 20 17:56:40 CET 2014

```Once you identify the number and identity of the non-native contacts (after
comparing the two matrices), then you can extract the probability of their

On Mon, Jan 20, 2014 at 8:23 PM, suhani nagpal <suhani.nagpal at gmail.com>wrote:

> okay.
>
> Basically i want to make a plot these non-native contacts information which
> are formed.
>
>
> Thanks
>
>
> On Mon, Jan 20, 2014 at 7:33 PM, bipin singh <bipinelmat at gmail.com> wrote:
>
> > >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
> > > > > 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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> > > > > --
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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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--

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