[gmx-users] non-native contatcs

[bipin singh]

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
>
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> School of Pharmacy
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-- 



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