AMBER Archive (2004)

Subject: Re: AMBER: LES

From: Petr Jeřábek (rowan_at_chemi.muni.cz)
Date: Thu Feb 19 2004 - 16:10:00 CST

Hallo Viktor,

in a regular MD the trichloropropane did not have a tendency go out from
protein. As I found during the heating phase arose same changes ( may be due
to rapid heating .. I dont know ) that probably did not allow the reversion
of the substrate to the reactive position.

Petr
 ----------------------------------------------------
   Petr Jeřábek
   National Centre for Biomolecular Research
   Masaryk University, Faculty of Science
   Kotlarska 2, 611 37 Brno, Czech Republic

   phone: +420732338613
   e-mail: rowan_at_chemi.muni.cz
   http://chemi.muni.cz/~rowan
 ----------------------------------------------------

----- Original Message -----
From: "Viktor Hornak" <hornak_at_csb.sunysb.edu>
To: <amber_at_scripps.edu>
Sent: Thursday, February 19, 2004 10:30 PM
Subject: Re: AMBER: LES

> 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...
>
> -Viktor
>
> Petr Jeřábek 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 Jeřábek
> > National Centre for Biomolecular Research
> > Masaryk University, Faculty of Science
> > Kotlarska 2, 611 37 Brno, Czech Republic
> >
> > phone: +420732338613
> > e-mail: rowan_at_chemi.muni.cz <mailto:rowan_at_chemi.muni.cz>
> > http://chemi.muni.cz/~rowan <http://chemi.muni.cz/%7Erowan>
> > ----------------------------------------------------
> >
> > ----- Original Message -----
> > *From:* Carlos Simmerling <mailto:carlos_at_csb.sunysb.edu>
> > *To:* amber_at_scripps.edu <mailto:amber_at_scripps.edu>
> > *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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