GROMACS version:2023
GROMACS modification: No
Hellos everyone
I am using charmm36_ljpme_jul2022 to simulate a protein-peptide interaction in gromacs. The protein has a zn2+ in binding sites and there are residue like two glu and two his which coordinates zn2+ . When I run pdb2gmx gromacs chose by default two different isoforms for those two his residues. One HID and one HIE, I was curious, should I change the his isomers types manually and change both to HID which NE atoms interact with zn?
Moreover, there two types of zn and cl entries defined in ions.itp in this force field, which one can better describe zn ions in protein binding sites?
Thanks for any help