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.