Dear all, I am working on studying the effect of a molecule on a protein. I am using CHARMM force-field in GROMACS for a protein (From literature studies and validation of protein properties, this force field was chosen) and I intend to study the effect of a molecule on the protein. The molecule taken was L-Ascorbic acid and I obtained the structure of the file through ZINC database, CSD and RCSB ligand database (Tried all 3 structures) . I obtained the topology files for CHARMM using (a) SWISSPDB (b) LigParGen and (c) ParamChem.org (Gives high penalties , hence I did not use this topology). In order to validate the force-field of this structure, I took a box of roughly 2000 molecules (L-Ascorbic acid) and ran a equilibriation, NVT and NPT (20ns). But, I am unable to obtain the desired density of the compound (Reported in literature = 1.65 g/cm3) , obtained density from my MD studies (1.48 g/cm3).
I have tried obtaining charges through semi-empirical DFT and used those charges as well. But I cannot obtain the density of the compound. This molecule exists as solid at the given conditions (P= 1 atm, T= 298 K). Should I look at any other property of the compound? If so, what properties could be validated for solids? I am aware that parametrization of a molecule is a tedious process. Should I go forward and try doing that? Or are there any more parameters or conditions that I have failed to look at?
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