[gmx-users] DSSP

[Nataraj B (ORLL-Biotech)]

           Shahid,
 
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
 
B.Nataraj
 
 
-----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
 
Hi
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.

http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp

-Justin
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
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at] vt.edu <http://vt.edu/>  | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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