[gmx-users] Re: change in secondary structure

[Justin A. Lemkul]

bharat gupta wrote:
> Hi,
> 
> I think I have asked this question earlier in the forum .. that during 
> my 3ns simulation of a 230 amino acid proteins some portion of 2 beta 
> strands got converted to loop/random coil, after visualizing in VMD. I 
> checked the DSSP profile also .. and as per the DSSP results it's coil 
> in that region .. can anybody tell me where can the error be as I have 
> been checking my structure right from the minimization step till npt 
> equilibration and its was fine ... this has happened only after 
> simulation ... pls help ?? 
> 

The comments I made last week still stand:

http://lists.gromacs.org/pipermail/gmx-users/2011-January/058014.html

You're basing your conclusions on a 3-ns simulation, which I would say is far 
too short to obtain any meaningful data for such a system.

-Justin

> -- 
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
> Division of Chemical Engineering and Polymer Science
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> Busan -609735
> South Korea
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> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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