[gmx-users] DSSP

Nataraj B (ORLL-Biotech) nataraj at orchidpharma.com
Tue May 18 14:06:05 CEST 2010

Before trying for "do_dssp" a gromacs utility calling dssp program , try first dssp program itself  by passing simple input like pdb and I hope by that way you can resolve your problem
-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]On Behalf Of shahid nayeem
Sent: Tuesday, May 18, 2010 5:17 PM
To: jalemkul at vt.edu; Discussion list for GROMACS users
Subject: Re: [gmx-users] DSSP
After posting this mail I did some google search and after changing the executible name to dssp I moved it in /usr/local/bin/ After this when I did do_dssp it starts running asks to select a group I choose main chain 5, then it generates some intermediate file and gives error as segmentation fault. I though this problem was because of the executible in /usr/local/bin/ and rest of file in another directory say /home/shahid/software/dssp/. For this first I set the path in ~/.bascrc as DSSP=/home/shahid/software/dssp/DsspCmbi. I tried to run do_dssp I got the same intermediate file generated backing up the previous one. Then I moved all the files of dssp directory to /usr/local/bin/ and then tried to run do_dssp I am in the same situation. 
waiting for your help
shahid nayeem

On 5/18/10, Justin A. Lemkul < jalemkul at vt.edu> wrote: 

shahid nayeem wrote:
Dear All
I downloaded dsspcmbi.tar.gz, and compiled  using command
./DsspCompileGCC as given in Readme.txt file. when I try to run
do_dssp command in gromacs I get error

Well, what happened?

Fatal error:
DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP)

I checked for DSSP executible in /usr/local/bin/ and I couldnt find. I

It won't be there unless you put it there and you have re-named it.  I believe the default name of the dssp program is "dsspcmbi," which you need to change when you move the executable.


even tried dsspcmbi.zip file but again I got the same error. I
compiled dssp as root. Now what shoul I do in order to run do_dssp
comand of gromacs.
Shahid nayeem


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at] vt.edu <http://vt.edu/>  | (540) 231-9080

gmx-users mailing list     gmx-users at gromacs.org
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100518/0d568107/attachment.html>

More information about the gromacs.org_gmx-users mailing list