Re: AMBER: Nudget Elastic Band query

From: Carlos Simmerling <>
Date: Thu, 5 Jul 2007 15:08:31 -0400

On 7/5/07, Francesco Pietra <> wrote:
> 90:10 population of conformers, ie 1.3 kcal/mol at rt, is an ideal
> situation
> for conformational studies (i.e NMR techniques can deal with so that one
> is not
> computing blind). Conformational energy differences are always in this
> range
> with natural products (or organic synthetic drugs). If MD can't deal with
> such
> energy differences, it will be of little use in this area and the
> interaction
> of with receptors. However, I vaguely remember of published MD dealing
> with
> such small energy differences. Perhaps I can find out the paper spending
> some
> time.

true, but my point was just that automatic parameters may not be good
I think most people use antechamber when they need lots of quick parameters
but for a single molecule where you want high accuracy you will probably
want to
at least check the parameters using high level QM.

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Received on Sun Jul 08 2007 - 06:07:29 PDT
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