AMBER Archive (2006)

Subject: Re: AMBER: antechamber

From: David Case (case_at_scripps.edu)
Date: Thu Jan 26 2006 - 17:48:55 CST

On Thu, Jan 26, 2006, ping jiang wrote:
>
> I am a new Amber user. Recently I met some problems
> when I used Antechamber probably because of my big
> molecule. The molecule that I used contains 1220
> atoms.

You are swimming upstream here. As a new amber user, you are attempting to
extend antechamber to a size of molecule that is an order of magnitude bigger
than what it (and the semiempirical quantum codes it calls) was designed for.

Antechamber is designed to work on small molecules, or on "residues" that are
parts of biomolecules. If you really need to look at thousand-atom molecules
that are not constructed of individual residues, you need to be prepared to
jump into the code, and to think hard about what you really want. Maybe you
can break your system into small pieces that antechamber can handle.

In any case, be sure you feel comfortable and experienced with these codes
on "ordinary-size" molecules before attempting to scale them up.

...regards...dac

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