On 1/13/20 9:15 AM, Sundari wrote:
Yes, Sir, I made the gro file for a particular time by using "gmx trjconv" command ( also checked with -pbc mol, whole, no_jump options ) but every time the 2ndary structure visualization in vmd is different from dssp sequence of residues in gromacs. Fox example in my protein dssp shows 8 residues making beta-sheets but when I load that particular time frame in vmd for visualizing the structure, these 8 residues showing 5-helix structure. Please suggest something.
I'm afraid I can't. Those are two completely different hydrogen bonding patterns and I can't imagine how the algorithms would differ so dramatically. I have seen VMD render coils for helices and sheets but never a totally different secondary structure. Be sure you're telling VMD to re-compute structures and re-color the secondary structure elements at every snapshot for trajectory visualization, otherwise it will render everything the same as the initial frame, which will obviously be wrong in the case of large structural changes.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
