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SchniedersLab / forcefieldx

Force Field X - Software for Molecular Biophysics
http://ffx.biochem.uiowa.edu/
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RMSD-PAC calculation #234

Open hazvzqhd opened 11 months ago

hazvzqhd commented 11 months ago

I'm interested in calculating the RMSD between two molecular crystals with the PAC algorithm; however, as I understand the information of the forcefield is required. Otherwise, I get the following error:

Oct 25, 2023 8:21:52 PM ffx.potential.bonded.Angle logNoAngleType SEVERE: No AngleType for key: 2 1 2

Therefore, I would like to know if the information of the force field is necessary and if it is, could you refer me to some documentation so I could understand how the calculations of the RMSD depends on this information?

anessler commented 11 months ago

Thank you very much for reaching out! I am sorry for the inconvenience. The atomic coordinates and force field are read in using FFX's System Filter which checks to ensure a reasonable force field has been supplied. While the PAC algorithm does not utilize the force field information, the methods that read in the coordinates are the same as those used for energies, minimizations, etc. I am in the process of implementing a "basic" force field to default to when no force field has been supplied and could bypass the force field requirements, however this is still a work in progress.

For now, the quickest approach is to generate fixed charge parameters for the molecule of interest. I would suggest the LigParGen server run by Professor Jorgensen out of Yale. Following the online generator, it should be relatively easy to produce fixed charge parameters in the TINKER format which is compatible with FFX.

If you continue to experience any issues, please feel free to reach out!

hazvzqhd commented 11 months ago

Thanks for the answer. I'll try your suggestion.