Hi Bob,
Just want to thank you again. I was able to temporarily change C_3 to C_R
using Jsmol on OSX and Safari.
Jen
On Tue, May 6, 2014 at 2:43 PM, Jenheta da silva <[email protected]> wrote:
> 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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>
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