Paul,
I need to clean that up on my page by trapping the zero partial charge on
alkanes. I don't know much about the calculation that Bob installed, but the
PUBCHEM_MMFF94_PARTIAL_CHARGES for alkanes are also zero. I was trapping those
files and making a slight adjustment to at least show the green surface that
suggests close to non-polar bonding. I broke this trap when I was adding the
dynamic MEP feature. Thanks for picking up on this.
Otis
--
Otis Rothenberger
[email protected]
http://chemagic.com
On May 11, 2012, at 10:47 AM, Pillot Paul wrote:
>> I've played with this new feature as well and I've found an unexpected
>> behavior : when the molecule is an alkane the VDW surface is not computed
>> and an error is issued, stating that the file does not contain partial
>> charges to display the MEP surface.
>>
>> The calculate partialcharge command runs just fine. Of course there are no
>> partial charges for these alkane models so that is certainly the cause for
>> the error.
>>
>>
>>
>> Nonetheless, in modelkit, if I create first a model with partial charges and
>> a MEP surface, and I subsequently remove from that model atoms or reduce
>> bonds order to get an alkane, then a green MEP surface is displayed.
>>
>>
>>
>> In Otis' page, this problem doesn't appear when one chooses to start from
>> C2H6 (green MEP surface is displayed). I suspect that's because the
>> ethene.txt file used there has charges set (-0.0680 for C and 0.0227 for H)
>> ... In Bob's "simple" page, this can be tested by loading ethan from NCI and
>> try to display MEP (no surface displayed).
>>
>> Paul
>>
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