From: Corey Fugate (
Date: Wed Apr 28 2010 - 23:17:39 CDT

        I am trying to use paratools to generate parameters for alanine. I'm
using alanine so I can come the parameters I generate to the
literature values.

        I setup a optimization, the file head is below-
# RHF/6-31G Opt=(Redundant) NoSymm Pop=(ESP,NPA) IOp(6/33=2) SCF=Tight

        I then use the optimized geometry to run the frequency calculation,
the file head is below-
# RHF/6-31G Geom=(AllCheck,NewRedundant) Freq NoSymm Pop=(ESP,NPA)
IOp(6/33=2,7/33=1) SCF=Tight

The first problem I am having is that in the topology file generated,
there are no charges on any of the atoms. In the VMD terminal output
when I'm loading in the files it says, "No mulliken charges found",
but I'm looking right at them in the log file! So why might I not be
seeing the charges and how do I get them in there?