From: bo baker (bo.bybaker_at_gmail.com)
Date: Wed Dec 17 2008 - 12:30:08 CST

Dear Axel and Peter:

Thank you for your advice.

In order to do QM Geometry optimization, one needs gaussian which is
not with VMD.

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

Thank you

Bo

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