[gmx-users] small molecule partial charges

[jxs818 at bham.ac.uk]

Hi All, 
I am working on a non standard ligand at the moment & 
wondered about defining partial charges on atoms. I have 
derived the partial charges using GAMESS with the 6-31G 
basis set. Can I just insert these into the .rtp file in 
the [ATOM] section for my ligand??? The other thing I was 
wondering was that GAMESS has assigned partial charges to 
carbon atoms in one of the alyl chains in the ligand, but 
looking through the .rtp file only a small small percentage 
of the alkyl carbons in the existing force field have a 
charge assigned to them. Do I leave these charges out?? 
Any help would be really gratefully accepted.
John