From: Axel Kohlmeyer (
Date: Wed Apr 28 2010 - 23:47:45 CDT

On Thu, Apr 29, 2010 at 12:17 AM, Corey Fugate <> wrote:
>        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-
> %mem=4GB
> %nproc=2
> %chk=ala52_opt.chk
> # 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-
> %mem=4GB
> %nproc=2
> %chk=ala52_sp.chk
> # 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?

you most likely use a different version of the quantum chemistry code
that paratools was tested with. those codes are notorious for changing
the output format in unpredictable ways all the time. that can easily
throw the parser in paratool off balance.

>                        Thanks,
>                                        Corey

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.