I want to see the fluctuation in the secondary structure elements in a protein after MD simulation at different time scale. Can anybody please let me know the step by step to install DSSP in CentOS.
For observing the secondary structure fluctuations over the time of trajectory, GROMACS already has a tool called do_dssp. Only thing you have to do is
1. Download DSSP executable for your system from DSSP site
2. Add path to DSSP executable to your PATH environment varibale
And that's it.. just run do_dssp gromacs command on your trajectory and you'll have graphs generated for sec str fluctuations..
Note: current DSSP version works with new gromcs 4.6 and 4.6.1. If you are using old gromacs, then you'll have dig out internet for old DSSP executables for your system. Best way is just to upgrade your gromacs to current version and it'll run properly the external DSSP comand
For observing the secondary structure fluctuations over the time of trajectory, GROMACS already has a tool called do_dssp. Only thing you have to do is
1. Download DSSP executable for your system from DSSP site
2. Add path to DSSP executable to your PATH environment varibale
And that's it.. just run do_dssp gromacs command on your trajectory and you'll have graphs generated for sec str fluctuations..
Note: current DSSP version works with new gromcs 4.6 and 4.6.1. If you are using old gromacs, then you'll have dig out internet for old DSSP executables for your system. Best way is just to upgrade your gromacs to current version and it'll run properly the external DSSP comand
Dear Jitendra,
Thank you very much for providing the valuable suggestion to install DSSP. Please let me know which version i should use and which executable file i will select. Thanking You in advance.
Hi Budheswar,
You can download current version of Gromacs i.e. 4.6.1 (http://www.gromacs.org/Downloads) and current version of dssp i.e. 2.0.4 (http://swift.cmbi.ru.nl/gv/dssp/) .. I have worked with these versions and they work good..
for installation you can use the installation instruction which is available here : http://www.gromacs.org/Documentation/Installation_Instructions
Jitesh
Thnakyou for the info, i have tried setting up dssp version 3.0.0 https://github.com/cmbi/xssp/releases to work with Gromacs ver 5.1.1 , but not able to set environment for the same.
Please help me with the same.
for installation you can use ftp://ftp.cmbi.ru.nl/pub/software/dssp/
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