[gmx-users] Secondary structure not visible after converting from .gro to .pdb

Justin Lemkul jalemkul at vt.edu
Thu May 29 03:30:06 CEST 2014

On 5/28/14, 9:24 PM, bharat gupta wrote:
> Hi,
> I energy minimized a protein consisting 10 chains using gromacs. When I
> converted the structure of the protein from gro format to pdb format to
> visualize in Pymol, it shows only one chain in ribbon form and rest of the
> chains are not shown ... How to rectify this error ??

Visualization programs guess what secondary structure should be based on the 
supplied geometry.  Sometimes they get it wrong.  If you're concerned about 
secondary structure changes, you should be using a quantitative method rather 
than visualization.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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