[gmx-users] Problem with DSSP

[Erik Marklund]

/home/dssp seems like a strange path. Are you sure you set DSSP correctly?

Erik
 
On 8 May 2013, at 15:19, Sainitin Donakonda <saigro16 at gmail.com> 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...*
> 
> *I have gone through gromacs list but unfortunately couldnot manage to
> solve this simple issue*
> 
> *
> *
> 
> *Thanks,*
> 
> *Nitin*
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