VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Wed Dec 17 2008 - 13:53:09 CST

On Thu, 18 Dec 2008, bo baker wrote:

BB> Dear Axel and Peter:
BB>
BB> Thank you for your advice.
BB>
BB> In order to do QM Geometry optimization, one needs gaussian which is
BB> not with VMD.

no, you don't _need_ gaussian. other quantum chemistry codes
should work as well. the problem is that you'll have to
adapt the input file.

BB> Gaussian is not free. Without Gaussian, one can't generate the top and
BB> para file by using paratool.

you could, you'd just have to adapt paratool to create proper
input files for some other QM code and teach it to parse the
resulting outputs. there is not much magic behind this. it only
takes some time and dedication. all the required steps can also
be done manually and are described in the corresponding papers
describing the parametrization process of the respective force
fields.

as i was writing before. this is not a task that can be done
without knowing what you are doing, anyways, regardless of the
QM code that you are using, or else you run a very high risk
of producing complete nonsense. paratool's purpose is to
aid in the process and automate some of the tedious tasks.

cheers,
   axel.

BB>
BB> Thank you
BB>
BB> Bo
BB>
BB> On 12/18/08, Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu> wrote:
BB> > On Wed, 17 Dec 2008, bo baker wrote:
BB> >
BB> > BB> Dear VMD:
BB> >
BB> > dear bo,
BB> >
BB> > BB> I try to use Paratool to generate top file for the ligand. From Setup
BB> > BB> QM Geometry optimization, a file named "xxx_opt.com is generated.
BB> > BB> Based on the Paratool tutorial, one needs to run the QM Geometry
BB> > BB> optimization by yourself. Here is my question: does the Paratool not
BB> > BB> have the function for QM Geometry optimization? If so, which program
BB> >
BB> > of course not! why would one want to do that? why reinvent
BB> > the wheel and write and maintain yet another QM program?
BB> > please also note, that if you are not familiar with running
BB> > QM calculations, it is advisable to first learn that, so
BB> > you can tell whether a calculation is successful or not.
BB> > same as for almost any calculation, there is some skill
BB> > and experience required to get correct results. all that
BB> > paratools is supposed to do is to make the rather tedious
BB> > job of setting up all those required calculation for
BB> > parametrizing a little bit easier.
BB> >
BB> > BB> shound one to use to do the QM Geometry optimization?
BB> >
BB> > please re-read the paratool documentation. it states very clearly
BB> > that paratool generates input files for gaussian.
BB> >
BB> > cheers,
BB> > axel.
BB> >
BB> >
BB> > BB>
BB> > BB> Thank you very much
BB> > BB>
BB> > BB> Bo
BB> > BB>
BB> >
BB> >
BB> > --
BB> > =======================================================================
BB> > Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
BB> > Center for Molecular Modeling -- University of Pennsylvania
BB> > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
BB> > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
BB> > =======================================================================
BB> > If you make something idiot-proof, the universe creates a better idiot.
BB> >
BB> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.