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
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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