for secondary structure analysis by gromacs 5.07 i need to install dssp but i dont know how i can install .please guide me
You can get it here: http://swift.cmbi.ru.nl/gv/dssp/
Go to Distribution in the left panel. Its an executable file. You need to download it and change its permissions (chmod a+x) and then export the path in your bash.rc file.
Yeah Nitika is right. In simpler terms it can be like,
1. Download DSSP executable from http://swift.cmbi.ru.nl/gv/dssp/
2. Place in the Bin folder
3. Give permission to execute (Right click -> properties -> Allow executable)
4. Add export path in "bashrc" file
Please follow the steps:
sudo wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-amd64 -O /usr/local/bin/dssp
or
sudo wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-i386 -O /usr/local/bin/dssp
Then:
sudo chmod a+x /usr/local/bin/dssp
i use from commands but when i want check secondary structure with this command:
do_dssp -f traj.xtc -s topol.tpr -o secondary-structure.xpm -sc secondary-structure.xvg -dt 10
i got this error:do-dssp not found
thanks for your guidance. after use from dssp i have a file which name is secondary structure's and its blur.how i can analyse this?
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salaam dostan man danshjoye olompezeshki tehran hastam mikham bebinam kodom ostad dakhel kodom daneshgah dar tehran gromacs ra dars mide khastam beram sare klasesh?
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