VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Oct 10 2012 - 14:53:19 CDT

John,
  If you read the source code for the VMD GAMESS plugin or the VMD
molecular orbital rendering code, I believe we have unit conversion
macros for computing Angstroms from Bohr and vice-versa. I'm away
from my desk so I can't tell you precisely, but I think that a
"grep -i bohr" in the VMD source code will find it for you.

Cheers,
 John

On Wed, Oct 10, 2012 at 11:50:00AM -0800, John Keller wrote:
> John,
> Thanks for the suggestion. If this OpenBabel idea pans out, I will post a
> message to that effect. Actually, Gaussian Inc consultants do have the
> beginnings of such a gawk script, however it stumbles over the fact that
> Gaussian dimensional units are given in Bohrs, while VMD is in Angstroms.
> I am scratching my head trying to reconcile these units presently. Again,
> if something comes of this, I will let you know.
> John
>
> ***************************************
> John W. Keller, Ph.D.
> Professor of Chemistry Emeritus
> Department of Chemistry & Biochemistry
> University of Alaska Fairbanks
> jwkeller_at_alaska.edu
> ***************************************
>
>
> On Wed, Oct 10, 2012 at 11:40 AM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> I'm not aware of any existing scripts or in-development Gaussian 09
> plugin updates, but you might look and see if the most recent versions
> of OpenBabel can read these files and convert them into something
> useful.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
> On Fri, Oct 05, 2012 at 02:06:49PM -0800, John Keller wrote:
> > Hi,
> > Does anyone know where one might find a script for reading the .log
> or
> > .fchk ouput file from a Gaussian ADMP molecular dynamics
> calculation into
> > VMD, or even if that is possible?
> > Thanks,
> > John Keller
> > Univ of Alaska Fairbanks
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078