[gmx-users] Problem executing do_dssp in gromacs

Justin Lemkul jalemkul at vt.edu
Mon Feb 16 19:23:06 CET 2015

After looking at this a bit more closely for someone else who asked the same 
question, your clue is here:

dssp cmd='/usr/local/bin/dssp -na dd31ZWbc ddI6at3a > /dev/null 2> /dev/null'

For some reason your do_dssp command is triggering version 1 syntax.  A version 
2 command should be something like:

dssp cmd='/usr/local/bin/dssp -i ddYB5REk -o ddxi1TAx > /dev/null 2> /dev/null'

Note the difference in -i/-o vs. -na.  This is the nature of the problem when 
dealing with different versions.  Somehow there's a disconnect between your DSSP 
version or the command you're telling us you're issuing.



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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