[gmx-users] Reg: creation of separate chains in .pdb file

Justin Lemkul jalemkul at vt.edu
Mon May 29 21:11:28 CEST 2017

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 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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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