PDB reading script outputs a value "tot_charge" which is the sum of all the element/atom charges from the PDB. Write_input adds that tot_charge and the specified seed charge to get the overall charge for a molecule. Works fine if the seed is a small molecule/non-canonical residue/anything that doesn't have any atom charges listed in the PDB but if there is a charged canonical amino acid (or anything that does have a charge listed in that column) then there is double counting in the overall charge in the input file. Need to modify how tot_charge is computed to ignore any charges on seed atoms in the pdb file.
PDB reading script outputs a value "tot_charge" which is the sum of all the element/atom charges from the PDB. Write_input adds that tot_charge and the specified seed charge to get the overall charge for a molecule. Works fine if the seed is a small molecule/non-canonical residue/anything that doesn't have any atom charges listed in the PDB but if there is a charged canonical amino acid (or anything that does have a charge listed in that column) then there is double counting in the overall charge in the input file. Need to modify how tot_charge is computed to ignore any charges on seed atoms in the pdb file.