Re: CCL:Amber7 and partial charges

From: David Case <>
Date: Wed 11 Dec 2002 10:07:10 -0800

On Tue, Dec 10, 2002, Carsten Detering wrote:
> I am struggling with assigning partial charges, which is my only interest
> at the moment. I have several RNA pdb files, to which I would like to assign
> partial charges and convert them to mol2 files on the fly. Following the
> manual, this can obviously be done with antechamber, however, the program
> core dumps every time I use it...

We would clearly need more information than this to be of much help: what
machine? does your version pass the test suite? what was the command line you
used? what was the input (pdb?) file?

> charges (esp) are only to be used for Gaussian.

If you have "ordinary" RNA nucleotides, then the charges are assigned from
a library in LEaP.

If you want the "automated" esp charges available from
antechamber, you need Gaussian (there's some recent stuff in the e-mail
archives with examples). The Amber web page has pointers to using GAMESS
(I beleive), and some people have tried Jaguar.

If you want the Am1-BCC charges, you would need a version of mopac (or
AMSOL) to do semiempirical calcs. The Users' Manual (installation section)
suggests places you can get these programs from.

...hope this helps...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
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Received on Wed Dec 11 2002 - 10:07:10 PST
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