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Here is the situation, I have trajecory file of a protein of interest. That protein has 2 main cavities that are participating in interraction with ligands or other proteins and also other cavities. Also residue numbers around this cavity are more or less known. I'm looking for a method or software to get volume of this cavities for every frame in trajectory.

I want to specify a cavity around a residue and get output for this cavity. What I am looking for is something like this:

Frame Cavity volume
1 1500 A^3
2 1499 A^3
3 1499 A^3
4 1499 A^3
5 1498 A^3

I tried CASTp, it was okey for singe frame if wrote it as pdb but not promising for a 100ns trajectory.

Also tried CAVER. CAVER was able to open a trajectory file and calculate cavity volumes for the frame that I chose but it was not possible to calculate cavity volumes for all of the frames and get output from it.

If anyone has any suggestion I'll be greatful.

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    $\begingroup$ If you can get one, then you can get many - it's just a matter of making right scripts for sequential initiation of program an gathering the output. $\endgroup$
    – Mithoron
    Commented Sep 11, 2019 at 13:56
  • $\begingroup$ @Mithoron Well I gladly would do that but It has graphical user interface so I dont know how can I do that. Also that program has problematic naming for cavities, for different frames same cavity has different names. If someone confirms it is possible with this software,then I'll dig for a solution. $\endgroup$
    – Onur Ozcan
    Commented Sep 11, 2019 at 14:59
  • $\begingroup$ @OnurOzcan CASTp seems to operate as a standalone webserver at which you have to submit your data, so it doesn't sound like a good solution. On the other hand the CAVER program seems to allow for analysis of a series of frames, see the examples that come with the program $\endgroup$
    – Buck Thorn ♦
    Commented Sep 11, 2019 at 16:15
  • $\begingroup$ They both provide pymol plugins, but the CASTp plugin is for visualization only. It may be possible to interact with the CAVER plugin using python. $\endgroup$
    – Buck Thorn ♦
    Commented Sep 11, 2019 at 16:17

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In short, POVME exactly does this.

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