[gmx-users] do_dssp problem

Mahboobeh Eslami mahboobeh.eslami at yahoo.com
Fri Oct 10 10:01:49 CEST 2014

dera mariannethanks for your replyI did not find version 1.0. i found only DSSPold of http://swift.cmbi.ru.nl/gv/dssp/)

Thank you sincerely for your help

     On Friday, October 10, 2014 11:19 AM, Marianne Schulte <Marianne.Schulte at uni-duesseldorf.de> wrote:

 Dear Mahboobeh,

did you try to specify your version? Maybe -ver 1.0 works.
Good luck!


On 10.10.14 09:39, Mahboobeh Eslami  <mahboobeh.eslami at yahoo.com> wrote:
hi dear justini use gromacs4.6.5  for protein-ligand complex simulationi wasn to study second structure of my protein for 20ns simulation. i used DSSP . I copied dssp file in /local/usr/bin and use following commandschmod +x dssp./dsspwhen i use following command:do_dssp -f md.xtc -s md.tpr -o md-ss.xpmi get following error:Failed to execute command: Try specifying your dssp version with the -ver option.i searched mailing list of gromacs and i found many similar question (http://comments.gmane.org/gmane.science.biology.gromacs.user/50170) and  
your answer is that use old version of DSSP so i downloaded dssp old version.i copy old vesion of dssp (dsspcmbi)  in /usr/local/bin and use following command "chmod +x dsspcmbi) and export path to bash (export DSSP=/usr/local/bin/dssp"
 but i get following error:
DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP)please help me.
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.


More information about the gromacs.org_gmx-users mailing list