[gmx-users] charge assign

[elham tazikeh]

Dear GMX users
i want to assign my ligand cherges by PRODRG

are these process be correct?

1. making *.pdb file by a server as chemspider: lig1.pdb

2.optimize my molecule in GUSSIAN by ordinary basis set:
lig1.gjf ......to......lig2.pdb

3.copy lig2.pdb in PRODRG and save the PDB*(all H s   or   polar/aromatic H
s)* as :lig3.pdb

4. calculate partial charges by NBO or MULICKEN method and making mlecule
as : lig4.pdb

5.copying cherges from lig4.pdb to lig.itp (the Gromacs topology from
PRODRG)


my question is in step 3: *all H s   or   polar/aromatic H  ???*

please help me
Regards