GROMACS modification: Yes/No
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I am currently trying to generate the .str file for the small molecule for MD. Using the CGenFF portal I am getting these above cut-off penalties for some. Somehow I minimized the structure using the MMFF94s and then tried again but the penalties remain the same. Then I tried optimizing my molecule by running through gamess and then again tried to get the .str seems like the penalties are worse this time.
I would like to get a general idea of penalties, and why are they getting imposed (higher penalties) on a simple molecule, as what I get from the CGenFF paper it seems as my molecule falls under the two broader categories (simple heterocyclic scaffolds and not some crazy functional groups).
How to get the penalties under 10? and if I doing so does it affects the integrity of the molecule?