CHARMM Development Project
Posted By: an_a Selenium containing ligand - 07/23/21 05:08 PM
I am working with a small molecule ligand that contains selenium. I am having trouble parameterizing it using CGenFF/ParamChem. I can't get it to successfully run through any of the parameterization options in CHARMM-GUI either. Does anyone have *any* experience with/advice regarding parameterizing and running MD of selenium containing small molecules? Any hints/suggestions would be very much appreciated!

Posted By: rmv Re: Selenium containing ligand - 07/23/21 07:08 PM
With a quick web search I found

Dataset of AMBER force field parameters of drugs, natural products and steroids for simulations using GROMACS.
Jennifer Loschwitz, Anna Jäckering, Monika Keutmann, Maryam Olagunju, Olujide O.Olubiyi, Birgit Strodel
Data in Brief,Volume 35, April 2021, 106948

They used GAFF to derive models using S instead of Se, defined some modified Se parameters, and changed S to Se after all the model building, which may be an approach to use with CGenFF and CHARMM-GUI. The Se parameters in that paper may or may not be transferrable, and should be validated before use with CHARMM force fields.
Posted By: an_a Re: Selenium containing ligand - 07/24/21 01:11 AM

Thank you very much for sharing this nice idea from the paper. This is perhaps what I will do as well. Seems like Se parameters are not available in many of the popular forcefields.

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