I am trying to do some MD simulations of a protein with zinc ions. I am trying to use a charmm forcefield (I have tried 2017 and 2021) and Gromacs.
I get an error when doing pdb2gmx
Residue 'ZN' not found in residue topology database
ZN is in the force field files for Charmm so I am not sure what to do!
Thanks in advance.
If Zn is forming a coordination complex then you will have to explicitly insert the bonds, angles, dihedrals, and improper in your topology with respect to coordinating residues of Zn.
A simple and quick way for you might be to use charmmGUI.
Hi Cassie! Please, check how Zn ions are called in the respective force field and make changes in names in the gro/pdb file, itp and top files. It can happen that in the forcefield ions are called as Zn and not ZN.
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