Re: [Jmol-users] Jmol partial charge calculation

[Paul P. <pau...@ac...>]

Thanks Otis !
I've just tried this trick by setting "{*}.partialcharge = 0.1; {*}.partialcharge=0.0" and it works (apparently there is no need to loop through all the atoms).
I solved my problem by just doing a simple check after "calculate partialCharge" and before isosurface creation :

if ({*}.partialcharge.min==0 && {*}.partialcharge.max==0) {{*}.partialcharge = 0.1; {*}.partialcharge=0.0}

Paul

Le 12 mai 2012 à 14:49, Otis Rothenberger a écrit :

> Paul,
> 
> This is one of those problems that I know how to fix, but I don't know why the fix works. For the PubChem alkanes (or any PubChem all zero atom charged molecules), here's how I fixed the problem:
> 
> if (jmolGetPropertyAsString("stateInfo").indexOf("PUBCHEM_MMFF94_PARTIAL_CHARGES") > -1) { mepsData = true; if (jmolEvaluate("{*}.partialCharge.max") == 0) { jmolScript('var x = {*}.size;var z="";for (var y = 1; y <= x; y++){{atomno = y}.partialCharge=0.1;{atomno = y}.partialCharge=0.0;}') } }
> 
> Focusing only on the jmolScript above, I first put a .1 partial charge on all the atoms. I then return all the values to 0.0. Why not set them all to 0.0 initially? It does not work! You have to set them to a non-zero value then reset them to zero. Needless to say, this was a trial and error discovery.
> 
> Anyway, I broke all of this in my attempt to set up dynamic MEP. I hope to have it all set up and fixed this week end.
> 
> Otis
> 
> 
> 
> --
> Otis Rothenberger
> ot...@ch...
> http://chemagic.com
> 
> 
> 
> 
> On May 12, 2012, at 3:54 AM, Paul Pillot wrote:
> 
>> Otis,
>> I think the green surface is great and I was just wondering how it could be displayed for alkanes. My guess is that it's not displayed because when there is no partial charge, no MEP surface can be created. The problem is "how does Jmol guess there is no partial charge in the file?", and the answer seems to be "when all partial charges are set to 0.0". This rule appears to work generally except for alkanes, even if it can look silly to search for polarity on alkanes !
>> Paul
>> 
>> Le 11 mai 2012 à 18:13, Otis Rothenberger a écrit :
>> 
>>> 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
>>> ot...@ch...
>>> 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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