[gmx-users] change in secondary structure after npt equilibration

[bharat gupta]

Hi,


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 ??

-- 
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
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