[gmx-users] Re: change in secondary structure

bharat gupta bharat.85.monu at gmail.com
Wed Feb 2 09:53:22 CET 2011


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 ??

Ph.D. Candidate
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