Ligand with Charge

[pealwl]

I would like to know what I should do if my ligand is charged in my protein-ligand complex. For example, the ligand has a -COOH group in it, and it is deprotonated in my ligand and becomes -COO⁻. If I run Uni-GBSA normally, it will give the following error:

Running: /home/username/anaconda3/envs/gbsa/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
Info: Total number of electrons: 71; net charge: 0
Info: The number of electrons is odd (71).
Please check the total charge (-nc flag) and spin multiplicity (-m flag).

which means that it assumes that the molecule is neutral and the molecule is a radical (-COO·). In this case, how can I specify the negative charge in Uni-GBSA?

Any help would be appreciated.

[Aunity]

You can try the command unigbsa-validate to fix this problem. But please double check the output file.