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. On Mon, Jan 13, 2020 at 7:01 PM Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/13/20 7:22 AM, Sundari wrote: > > Hello Dear, > > > > Actually I was thinking the same i.e. gromacs use "dssp" criteria and vmd > > use "stride" algorithm for secondary structure determination. > > But the expected error in the two algorithms should not be more than 5% > > according to the literature. Here, In my case, the structure contains a > lot > > of beta-sheets by dssp and that sequence in vmd is showing 5-helix > instead > > of beta-sheets. I am in a confusion now because I want the snapshots of > the > > structures obtained by gromacs dssp. > > Are you sure you're looking at the same snapshots? Those are wildly > different structures. I have had VMD show coils for helices and strands > before, but never any disagreement to this extent. > > -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. > -- 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.