[gmx-users] Problem with DSSP

Sainitin Donakonda saigro16 at gmail.com
Wed May 8 15:19:15 CEST 2013


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

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*




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