VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Wed Oct 10 2012 - 15:57:55 CDT

Race you to it!

Ang to Bohr is 1.88972612478289694072

Chris

On Oct 10, 2012, at 2:53 PM, John Stone wrote:

> 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