Hi all,

I have successfully derived partial charges using RED for two separate zinc binding domains in a protein. All the settings were carefully selected for the Amber sb99 FF and the structure was taken from the protein crystal structure. Restrained fitting was applied so the whole structure (minus capped termini to fit in with the peptide backbone bonding structure) will have a charge of zero. 

In the gromacs topology files I think could simply combine all four amino acids and Zn (3 his, 1 glu and zinc) and replace their usual partial charge with the newly derived ones. My question is whether this is enough? Besides the alterations to the partial charges, all other parameters for HIS, GLU and Zn are in the FF, surely? 

Many thanks,

Anthony