[gmx-users] dssp_index file

Justin Lemkul jalemkul at vt.edu
Mon Aug 25 20:12:47 CEST 2014

On 8/25/14, 2:09 PM, Ahmet Yıldırım wrote:
> I am using Gromacs 4.5.5 and old dssp (not dssp 2.x). Dssp is exist in usr/local/bin/dssp. It is executable.
> I dont have any error when I used the following command:
> do_dssp -f traj.xtc -s topol.tpr
> Select a group: 1 (protein)
> But I get the error when I used the index file with do_dssp. The index file includes a helix. I think dssp doesnt do the analysis of a helix/betasheet/coil...?

If it fails when running your index group, that indicates the contents of the 
group are invalid or in some way problematic.  How did you create the group? 
What is in it?



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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