Birgit-
Those mol2 files probably already have partial charges. To make matters worse,
not all partial charge calculations are the same. That’s going to affect color
and color range. Jmol uses MMFF94 charges.
In my own case, I prefer uniformity in my app, so I go with only Jmol with the
following script:
{*}.partialcharge=0.01;select *;calculate partialcharge;select *;isosurface
resolution 0 vdw color range -.07 .07 map mep translucent;
1) {*}.partialcharge=0.01 may not be needed. This is old code, and in the past
I needed it. It sets all existing partial charges to 0.01. I use 0.01 because
long ago 0 created a problem. These are all recalculated by Jmol.
2) color range -.07 .07 allows you to play with the charge range of the color
extremes. These values (-.07 .07) work well with MMFF94.
There is one exception. With spartan files, I don’t do this, but that’s another
story.
Otis
--
Otis Rothenberger
o...@chemagic.org
http://chemagic.org
> On May 1, 2016, at 3:08 PM, Birgit Lachner <bir...@lachner-net.de> wrote:
>
> Dear Robert and Angel,
>
> your informations are really very interessting. The two commands to calculate
> and show the MEP ist really easy. But I still have a problem to get the
> mol2-file.
>
> I usually use Avogadro for drawing and then I can save it in different
> formats. I can even calculate in Avogardo a MEP-map but it doesn't look nice.
> After saving it as mol2-file and opening it in Jmol I can use the scripting
> command
>
> - isosurface vdw map mep
>
> to shop the saved MEP informations. But they looks different from the one, I
> get calculated inside Jmol with
>
> - calculate partialcharge
>
> The colour range differs, e.g. no red and blue areas but only a shine of red
> and blue. This is even shown by the output of the console.
>
> I tried to calculate the MEP and save the file as a mol2-file but it was not
> successful. When I try to reopen it in Jmol I can't see the molecule anymore.
> Even when I saved the file at Avogadro as a mol2 file, opened in Jmol,
> calculated it in Jmol and saved the file again, I was not successful to use
> the MEP information.
>
> So, is there a chance to save the MEP informations calculated in Jmol in a
> mol2 file format? What is my error?
>
> Thanks, Birgit
>
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