[gmx-users] Problem with DSSP

[Justin Lemkul]

On 5/8/13 9:19 AM, Sainitin Donakonda wrote:
> Hello,
>
> I am trying to secondary structure analysis using DSSP in gromacs so i
> followed this procedure
>
> First I downloaded dssp
>
> wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-amd64  -O
> ~/dssp
>
> this gave dssp executable file in my home directory
>
> I checked ./dssp ...it works
>
> Then i set environment variable as follows
>
> export DSSP=/myhomedir/dssp/dssp
>
> then i executed following command in gromacs
>
> do_dssp -f protein.xtc -s protein.tpr -sc scount.xvg -o ss.xpm -dt 10
>
> But this gives following error
>
> *Program do_dssp, VERSION 4.5.4
> Source code file:
> /home/toor/gromacs/gromacs-4.5.4/src/tools/do_dssp.c, line: 516
>
> Fatal error:
> DSSP executable (/home/dssp) does not exist (use setenv DSSP)*
>
> *
> *
>
> *Can any body explain where it went wrong...*
>

Apparently you set the environment variable wrong.  When reporting problems, 
please be exact.  You have an export statement above that does not match what 
do_dssp actually finds.  We don't know where your files are or how you've 
organized things.  The DSSP environment variable needs to point to the dssp 
executable itself, not the directory containing it.

-Justin

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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