Custom force field

[obasekigit]

Good day, please is it possible to use a custom force to parameterize my protein? For example I'm working with a phosphorylated amino acid.

[lohedges]

Hello there. What kind of customisation do you require? If it's modification or addition to existing AMBER force field parameters then this could be achieved with the pre_mol_commands keyword argument in any of the AMBER protein force field functions, e.g. as described here. This could be used to source an additional parameter file.

[obasekigit]

I have a charmm customized topology and parameter file and would like to use biosimspace to set up my simulation

[lohedges]

Okay, as a first test just try reading them. (Assuming a PSF, a parameter file, and PDB for coordinates.) We do have a CharmmPSF parser but it doesn't support everything.