Re: [AMBER] assignment of partial charge to fullerene2160

From: FyD <>
Date: Tue, 27 Mar 2012 14:55:04 +0200

Dear Gargi Borgohai,

If I understand you, you assigned 'manually' charge values to atoms...
If so, I think this is quite dangerous. At least to get some idea
about charge values in your fullerene case, you could look at ESP
charge values generated by GAMESS/Gaussian or Firefly when using the
CHELPG or Connolly surface algorithm (these charge values are NOT made
equivalent by the QM program)... This could guide you what could be
the charge values for the carbon atoms...

More generally, if all the atoms are chemically equivalent this likely
means that all the charge values should equal zero (I wonder if this
was not already discussed in the Amber mailing list).

regards, Francois

> I am trying to generate polar confinement using
> fullerene2160. To do so I assigned some charge values ( both positive
> (+0.15e) and negative (-0.15e) so that ultimate charge of the molecule
> becomes zero) to the mol2 file. Then I loaded the mol2 file at XLEaP and
> saved the .prmtop and .inpcrd files. After that when I minimised the
> structure and saved the pdb file in order to visualize the structure with
> VMD then the structure showed that all carbon atoms are detached from each
> other i.e. fullerene ball contained only carbon atoms and not any bond. The
> input file I used for minimization:

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Received on Tue Mar 27 2012 - 06:00:04 PDT
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