Dear Amber Users,
I hope this message finds you well. I am reaching out to inquire if anyone is utilizing automated tools for torsional re-parameterization to refine GAFF/GAFF2 torsional parameters. From my experience, the tools available in AmberTools seem inadequate for large-scale applications.
We have observed that using off-the-shelf GAFF parameters for ligand-binding free energy estimation can sometimes yield results that are even less accurate than docking.
I would appreciate any insight or recommendations regarding successful workflows. I’ve come across the AFFDO code and reached out to the developers but have not received a response, so I’m turning to the community for alternative solutions.
Currently, I rely on GROMACS tools, but the output I’m using isn’t easily portable to standard AMBER formats. Any suggestions or advice would be highly appreciated.
Kind regards,Marawan
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Received on Sun Oct 20 2024 - 10:30:02 PDT
