AMBER Archive (2009)
Subject: Re: [AMBER] max atoms for antechamber
From: Alan (alanwilter_at_gmail.com)
Date: Mon Jun 22 2009 - 08:00:48 CDT
I am aware of the issues related to Mopac. Anyway, it's good to have
figure in mind.
On Mon, Jun 22, 2009 at 13:48, case<case_at_biomaps.rutgers.edu> wrote:
> On Mon, Jun 22, 2009, Alan wrote:
>> What would be the (either roughly or recommended) max number of atoms
>> for antechamber?
> Maybe 100 or 200 atoms. The problem is not allocating memory, per se. It is
> more that (1) a quantum calculation is needed to obtain partial charges, and
> one is more likely to have problems (such as SCF conversion) with big
> molecules; furthermore, the charge model itself was designed for smallish
> molecules, and one doesn't know what sort of performance to expect with large
> systems. (2) antechamber has to infer the bonding characteristics from the
> geometry, and the number of possibilities grows with the size of the molecule.
> AMBER mailing list
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
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