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
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 : [email protected] <mailto:[email protected]>
--
========================================
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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