[gmx-users] Problem running do_dssp

Justin Lemkul jalemkul at vt.edu
Mon Aug 12 22:41:47 CEST 2013

On 8/12/13 4:29 PM, Dipankar Roy wrote:
> Hi,
> I am trying to use do_dssp to generate a secondary structure map over time for a 10-ns simulation. I have installed dssp_2.2.0 at the usual /usr/local/bin
> I tried running it with the following command line
> do_dssp -f md.xtc -s md.tpr -o ss.xpm -sc ss.xvg -dt 100 -tu ps; but ended up with the following error.
> Thanks in advance for your help.
> Selected 4: 'Backbone'
> There are 424 residues in your selected group
> dssp cmd='/usr/local/bin/dssp -i dd5Yvoh4 -o ddazDUUO > /dev/null 2> /dev/null'
> Reading frame       0 time    0.000
> Back Off! I just backed up dd5Yvoh4 to ./#dd5Yvoh4.1#
> -------------------------------------------------------
> Program do_dssp, VERSION 4.6.3
> Source code file: /home/rsd/gromacs-4.6.3/src/tools/gmx_do_dssp.c, line: 669
> Fatal error:
> Failed to execute command: Try specifying your dssp version with the -ver option.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> "God is a DJ" (Faithless)

This issue has been discussed numerous times (hint: check the archive, it will 
save you time!) and the solution is shown in the fatal error.  DSSP has 
different syntax in different versions.  If you have dssp-2.2.0, use "-ver 2" in 
the do_dssp command.  Also note that Backbone will not work because DSSP 
requires carbonyl oxygen atoms to determine hydrogen bonding patterns.  You need 
to choose, at minimum, MainChain.



Justin A. Lemkul, Ph.D.
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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