Re: [AMBER] assigning atom type and charge

From: FyD <>
Date: Thu, 09 Jul 2015 08:51:58 +0000

Dear Sanjib,

> I am working on carbon nanotube. It is about
> 100 angstrom long and contains 984 atoms. Now I want to assign atom type
> 'CA' and charge '0.0' to each and every carbon atom. As per my knowledge,
> it can be done in xleap unit editor after uploading the molecule in xleap
> and then selecting all atoms. But it will be very huge task as this
> molecule contains around 1000 atoms. Therefore I want to know if there is
> any other way to assign atom type and charges to all atoms so that I can do
> this job little easily.

You could use PyRED at R.E.D. Server Dev...

Chemical equivalencing & atom typing for carbon nanotubes is very
robust in PyRED from our tests...
(I do not think Antechamber handle these cases)

Obviously there are limits at R.E.D. Server Dev.
but these limits can be postponed and the different options of OPT_Calc
in the System.config file can also help
i.e. OPT_Calc = On2

better using the last version of Gaussian here; so creating a private

regards, Francois

           F.-Y. Dupradeau

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Received on Thu Jul 09 2015 - 02:00:03 PDT
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