How to do secondary structure analysis from the MD trajectory using DSSP program?

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Uttam Pal

You can do it in VMD. There's a very good tool for timeline analysis (Extension->Analysis->Timeline). Just load the structure, load the trajectory. Then open the timeline window and in there you will find the Calc. Sec. Struct option under Calculate menu.

Bikash Ranjan Sahoo

Thanx Mr. Uttam Pal. I used to do this in VMD. But for large size cycle files the graphics is not working. So I am trying to do it in DSSP. However I think I need license for this. I wanted to perform in DSSP this time. So searching for some information. Anyway thanx for ur reply.

Regards

Bikash

Rajendra Kumar

At first you have to install dssp. If it is installed in standard location such as /usr/local/bin/dssp, it would work. If it is installed in other location, then you have to define dssp environment variable like "export DSSP /path/to/dssp". Please, go through "do_dssp -h" for more details.

Newer version of dssp is available for the download. You can get in the following link: http://swift.cmbi.ru.nl/gv/dssp/ . Please follow discussion in Gromacs mailing list : http://lists.gromacs.org/pipermail/gmx-users/2012-November/076299.html .