.str files

GROMACS version: 2018.1
GROMACS modification: Yes/No
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I have generated the .str file for a small organic compound, using the CHARMM General Force Field server. However, I am getting a high number of penalties in the produced. I have previously optimized the geometry of my structure using Avogadro, but that doesn’t seem to work. I realize that this is not a problem of GROMACS, but I do need a solution. I have also downloaded the FFParam GUI server, but I cannot understand if I am doing the procedure the correct way. Thank you in advance.

FFParam has tutorials and the CGenFF paper from 2010 is itself a case study in how to parametrize a molecule. Parametrization with the CHARMM or CGenFF force field requires a combination of QM and MM calculations, for which GROMACS is not particularly well suited.