On 6/1/17 4:30 AM, Syed Azeem wrote:
On 5/31/17 8:26 AM, Syed Azeem wrote:
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.
Hey Justin,
I tried adding chain identifiers naming A & B to the file. It creates
another linear peptide chain away from main complex, when I view it in
Pymol.
Sounds like a periodicity issue. PyMOL is only telling you what's there;
it's
not "creating" anything :)
Hey Justin,
How do I overcome this periodicity issue?
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow
If I had a nickel for every time I've posted that link...
-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
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