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
After much digging I think I might be on the right track. I simply can't change the partial charges of those four amino acids and zinc in the topology file for my system. The charge in each group would be uneven. Rather I should define a new aminoacid type in the forcefield (aminoacids.rpt), e.g., STRZN (structural zinc) and add in three copies of HIS, one of GLU followed by ZN.
- Badges
- Science topic