[gmx-users] non-native contatcs

[Justin Lemkul]

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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