Charmm36 does not recognize CU atom

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1

Hi all,
I am going to use Charmm36 2020 to prepare human superoxide dismutase 3 (PDB ID 2JLP). However, the force field does not recognize CU atom.
How this problem can be fixed?

Yours,
-Sara

2

Hi,
the atomtype CU is defined in CHARMM36 port for GROMACS. Probably the issue is different. Where did you get the error and what error do you get?
Alessandra

3

CHARMM supports elemental copper (via an auxiliary parameter set) but does not officially support Cu2+. There are parameters available from dx.doi.org/10.1021/jp309150r that could be used, but these have never been formally evaluated for compatibility with the protein force field.

4

thanks for your reply. I have got the error following pdb2gmx command. the error just says that CU atom is unknow.

6

Thank you very much for your response. Now I have the same problem with ZN atom.