how to calculate entropy from other than .psf or .dcd file

[Rajeev Roy]

Hi everybody,

I am a new user, I have used Desmond software from http://www.deshawresearch.com/ research group for MD simulation, now I want to calculate entropy of the ligand, while searching for the appropriate program I came to know about Carma, but Desmond is not generating .psf or .dcd file. I am wondering how I should proceed.

I need guidance, please help me.

[Nicholas M Glykos]

> I am a new user, I have used Desmond software from
> http://www.deshawresearch.com/ research group for MD simulation, now I want
> to calculate entropy of the ligand, while searching for the appropriate
> program I came to know about Carma, but Desmond is not generating .psf or
> .dcd file. I am wondering how I should proceed.

You'll have to go through format conversions. catdcd and VMD probably have
plugins to convert from desmond to DCD. You can produce a PSF file (that
should exactly match the contents of the DCD) from a PDB file using VMD.




--


Nicholas M. Glykos, Department of Molecular Biology
and Genetics, Democritus University of Thrace, University Campus,
Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/

[Rajeev Roy]

Thank you very much Sir, for your reply.