LES definitely weakens the interactions. heating will make it
dissociate unless you put on some distance restraints or
something to keep it nearby.
are you trying to optimize the docked conformation without
letting it dissociate? then the restraints might be good
or keep the T lower than with regular MD. using the
separate temperature bath for LES might help too, keep
the protein at 300K and LES regions at lower T using TEMP0LES.
Carlos
----- Original Message -----
From: "Petr Jeřábek" <rowan.chemi.muni.cz>
To: <amber.scripps.edu>
Sent: Thursday, February 19, 2004 5:10 PM
Subject: Re: AMBER: LES
> 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.chemi.muni.cz
> http://chemi.muni.cz/~rowan
> ----------------------------------------------------
>
> ----- Original Message -----
> From: "Viktor Hornak" <hornak.csb.sunysb.edu>
> To: <amber.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.chemi.muni.cz <mailto:rowan.chemi.muni.cz>
> > > http://chemi.muni.cz/~rowan <http://chemi.muni.cz/%7Erowan>
> > > ----------------------------------------------------
> > >
> > > ----- Original Message -----
> > > *From:* Carlos Simmerling <mailto:carlos.csb.sunysb.edu>
> > > *To:* amber.scripps.edu <mailto:amber.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.
> > >
> > >
> >
> >
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber.scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> >
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Thu Feb 19 2004 - 22:53:00 PST
