[gmx-users] charge assign

[elham tazikeh]

Dear Justin
i really appreciate for your reply
i think my question wasn't clear. i prefer to express my problem again:

i'd like to accomplish protein-drug simulation by gromos force field and
before, docked my ligand on the protein (because,there wasn't the
crystallography file of this complex).
Now, to reach my destination, i eliminated ligand.pdb file from the end of
the complex.pdb and determined the charges of atoms by gaussian software by
mulicken method  (without optimization ), but the numbers of atoms in this
file and the files come from PRODRG server (the gromaces 87/gromacs
coordinate file .polar /aromatic hydrogens (*.gro) and the gromaces
topology (*.itp)) weren't the same.
 for this reason, i pasted the section of complex.pdb as lig.pdb in PRODRG
and achieved all formats of my ligand.
next, i saved the pdb file (polar/aromatic hydrogens) as ligand.pdb and
then give it to gaussian software to determination the charge of atoms.

Is it correct?
or
i should adding hydrogens to my ligand by another way?


Regards
elham