VMD-L Mailing List

From: Corey Fugate (fugate_at_hawaii.edu)
Date: Thu Apr 29 2010 - 01:35:23 CDT

Alright, so can I just put in the mulliken charges into the partial
charges of the topology file? No I cannot. I have to develop the
mulliken charges into CHARMM style charges as described in the
paratool user's guide.

Another question, When capping the ends of the amino acid, is it best
to cap with a methyl group?

                Thanks,
                                Corey

On Apr 28, 2010, at 6:47 PM, Axel Kohlmeyer wrote:

> On Thu, Apr 29, 2010 at 12:17 AM, Corey Fugate <fugate_at_hawaii.edu>
> 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.
>
> cheers,
> axel.
>>
>> Thanks,
>>
>> Corey
>>
>>
>>
>>
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> http://sites.google.com/site/akohlmey/
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>