Thank you, Bob.
I found the UFF.dat file buried in the folder
jsmol/j2s/J/minimize/forcefield/data
This is the one, right ?
Unfortunately, I could not give a shot of your suggestion yet due to some
issues when loading jsmol (there is a javascript alert about an unexpected
identifier j2s/core/corescript.z.js and an error
"network_err:XMLHttpRequest Exception 101") at my
fedora box. I am working on this now.
Best,
Jen
On Mon, May 5, 2014 at 7:05 PM, Robert Hanson <[email protected]> wrote:
> It's certainly possible in JavaScript; less so in Java. In
>
> jsmol/j2s/JM/ff/UFF.txt
>
> change
>
> atom [c] C_R aromatic C
>
> to
>
> atom [#6] C_R aromatic C
>
> This will cause ALL carbons to be aromatic, so don't leave it like this!
>
>
> Bob
>
>
>
> On Mon, May 5, 2014 at 1:31 PM, Jenheta da silva <[email protected]>wrote:
>
>> Dear Jmol users,
>>
>> I loaded a single xyz structure of C60 into Jmol (older and latest
>> versions),
>> in order to extract UFF intramolecular bonding parameters.
>> Thanks to an older post from Bob, this was an easy step :
>>
>> set loglevel 6
>> minimize steps 0
>> x = script("show minimization")
>> print x
>> set debug off
>>
>> which, from the related output, Jmol identified all carbon atoms as being
>> of type C_3. Is there some way to set the atom type from C_3 to C_R ?
>>
>> Thanks for any suggestions.
>>
>> Sincerely,
>> Jen
>>
>>
>>
>>
>>
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>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>
>
> ------------------------------------------------------------------------------
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> out:
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