On 5/29/17 8:00 AM, Syed Azeem wrote:
Hey all, I simulated a protein-peptide docked complex. Post simulation, I created an index file selecting only the Protein Group (protein-peptide complex). Then using editconf, I created a .pdb file for the same. When I view the prtn.pdb file, only the protein is available but not the peptide. Still the prtn.pdb file has coordinates for peptide as well. The pdb file also lacks a chain identifier, which was present in
If you're having trouble viewing the coordinates, that's a problem with the viewer itself. You say that the coordinates are there (as they should be) so there's no reason they can't be visualized if rendered properly.
the initial structure. How to overcome this?
Add suitable chain identifiers back into the coordinate file. -Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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.
