rbcavity extremely slow when used to identify all possible cavities in an RNA structure
Dear team,
I have been trying to use rbcavity as a RNA-specific pocket prediction method, to identify all possible cavities in an RNA structure. When the RNA structure is large (more than 100 nucleotides), I find that rbcavity takes very long time to complete writing the .grd files. For example, for PDB ID: 4FAW, I got 8 cavities using the two sphere method, with the radius set to cover the entire RNA. The program has been running for past 1 hour and is yet to complete writing the .grd files for the 8 cavities. I am using Ubuntu 22.04.5 LTS in an 8 core CPU machine. I faced similar issue with another machine as well for the same RNA - Ubuntu 22.04.5 LTS and with 16 cores. How can I make rbcavity faster for larger structures? Is there any specific memory requirement to run the program? Your suggestions will be very helpful for me to use the program for my current project.
With regards, Sowmya