Custom Amino Acid Partial Charge Assignment

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1

Hello,

I have been working to generate parameters for a post-translationally modified Histidine residue for use in GROMACS simulations. I started from an experimentally determined PDB file, adjusted bonds in Avogadro2, and parameterized with the CGenFF server. I then manually removed the HXT and OXT atoms and adjusted the C, CA, N, and O atom types and charges to match the standard amino acid backbone parameters found in the CHARMM force field. However, these adjustments resulted in a residue with a net charge of about -0.063. My two questions are:

  1. Is there a way to assign partial charges for the rest of the residue while restraining the backbone charges to the “standard” values?

  2. Otherwise, is it acceptable to go ahead with simulation using “non-standard” partial charge assignments for my residues backbone atoms?

Thanks for any feedback!