Coverting multi-frame .pdb file to .dcd and .psf files for entropy calculation

[Anupam Banerjee]

Hello,

I want to compute the protein's entropy using the −TEMPERATURE <FLOAT> flag. However, I only have the multi frame trajectory information of the CAlpha atoms in the .pdb format generated by Normal Mode Analysis. I wanted to know whether it is possible to compute the entropy in such cases and how do I generate the .dcd and .psf file from the existing multi-frame pdb file.

With best regards,
Anupam

[Nicholas M Glykos]

> I want to compute the protein's entropy using the яяTEMPERATURE <FLOAT>

> flag. However, I only have the multi frame trajectory information of the
> CAlpha atoms in the .pdb format generated by Normal Mode Analysis. I wanted
> to know whether it is possible to compute the entropy in such cases and how
> do I generate the .dcd and .psf file from the existing multi-frame pdb file.

VMD can do the conversion and carma will probably perform the requested
entropy calculation. Now, whether it is meaningful to only use CA atoms
obtained for a normal mode analysis it is a completely different subject.




--


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, https://utopia.duth.gr/glykos/

[Nicholas M. Glykos]

Quoting Anupam Banerjee <mr.anupa...@gmail.com>:

> Hey,
>
> Thanks a lot for your prompt reply. I searched for ways to convert a
> multi-frame .pdb file to .dcd format in VMD but I couldn't get hold of any
> such process (there are a lot of links for .dcd to .pdb transformation). It
> will be really kind of you if you could provide a link (or mention a
> command) that explains the same
>
> WIth best regards,
> Anupam

[Nicholas M. Glykos]

> Thanks a lot for your prompt reply. I searched for ways to convert a
> multi-frame .pdb file to .dcd format in VMD but I couldn't get hold of any
> such process (there are a lot of links for .dcd to .pdb transformation). It
> will be really kind of you if you could provide a link (or mention a
> command) that explains the same

VMD superposition.pdb -> Select superposition.pdb -> File -> Save
coordinates -> File type DCD -> Save