[gmx-users] Re: change in secondary structure

[bharat gupta]

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 ??

-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46010 at yahoo.com
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110202/bdfa3f96/attachment.html>