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cbc-univie / transformato

Set up relative free energy calculations using a common scaffold
https://cbc-univie.github.io/transformato/
MIT License
22 stars 6 forks source link

Alternate system inputs #115

Open ljmartin opened 1 year ago

ljmartin commented 1 year ago

Hi Transformato - looking forward to using this package. Thanks for making it available.

I'm interested in using this with inputs other than those that come from CHARMM-GUI, and/or that don't use CGenFF. Since the MD core looks like it is OpenMM, that means AMBER-style and GROMACS-style inputs are on the table. As far as I can see, the key step is generating a "SystemStructure" object: https://github.com/wiederm/transformato/blob/77d5f0fd2e3e9a0d67c0ecc817bfe8389295a3aa/transformato/system.py#L16 which, right now, uses a lot of psf-specific data. But perhaps it's doable to port this to work on an openmm or parmed topology, instead. Is this something that's already on your radar for implementation? Can you see any roadblocks if I start trying now? Thanks

JohannesKarwou commented 1 year ago

Hi,

Sorry for the late response!

Other input than CHARMM-GUI should not be a problem if you use CGenFF. In this case, you only need to provide a psf file and crd file in the folder called openmm.

Yes you are correct, currently we use the psf file and modify it during the process, this is all done with parmed. I think it should be doable to implement support for the amber force field by reading in the corresponding topology (as far as I understand AMBER, that would be the parm7 file). I'm currently working on supporting AMBER, but this might take some time. Feel free to take a look at the corresponding PR https://github.com/wiederm/transformato/pull/116 - input or feedback is always appreciated!