AMBER Archive (2004)

Subject: Re: AMBER: LES

From: Viktor Hornak (
Date: Thu Feb 19 2004 - 15:30:32 CST

Dear Petr,

I would also try to understand why your substrate has a tendency to
difuse from the binding site (trichloropropane parametrization?). If you
cannot keep it in place in a regular MD (and you know it should be
there), using LES will not help in any way...


Petr Jebek wrote:

> as I wrote, I have a protein of haloakane dehalogenase with small
> substrate trichlorpropane. From docking, I have got three different
> positions of this substrate in the active site of the enzyme and I
> would like to know what is the percentage occurrence of this positions
> during the simulation. In the previous simulations substrate had
> tendency to go out from protein ( but from experimental studies is
> clear that trichloropropane is reactive ).
> ----------------------------------------------------
> Petr Jebek
> National Centre for Biomolecular Research
> Masaryk University, Faculty of Science
> Kotlarska 2, 611 37 Brno, Czech Republic
> phone: +420732338613
> e-mail: <>
> <>
> ----------------------------------------------------
> ----- Original Message -----
> *From:* Carlos Simmerling <>
> *To:* <>
> *Sent:* Thursday, February 19, 2004 9:26 PM
> *Subject:* Re: AMBER: LES
> it _really_ depends on what you're trying to study for your
> system. It isn't clear what you're trying to do. The time of the
> simulation also depends on what you're trying to do and the system
> properties. If you're trying to optimize structure, it can help to
> try several annealing protocols and see if the results are sensitive.
> With LES, you can look to see if the copies converge at the end of
> the
> annealing, or if they anneal to different conformations.

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