[gmx-users] Re : Change in secondary structure during the npt equilibration

bharat gupta bharat.85.monu at gmail.com
Fri Jan 28 10:57:38 CET 2011


I am doing a simulation of a 230 amino acid protein for 3ns ... and I have
completed the npt equilibration step .. After retrieving the structure from
npt step and viewing it in pymol, reveals that some portion of the beta
strand got changed to a loop but when I visualized the same structure in VMD
I found that nothing has happened to the structure .. In order to confirm
more ... I generated the SS profile using dssp and I found that , the dssp
shows E i.e. sheet for that region .. So what shall i do next ... shall I
continue with the production step or not ??

Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
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E-mail : monu46010 at yahoo.com
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