I don't think tmd is the right approch to determining relative populations of alternate
docked ligand poses. Perhaps something like MM-PBSA would be better.
tmd may be useful in understanding how the ligand moves from one location
to another, but it doesn't sound like the path is what you want. it sounds like
you want relative binding free energies.
carlos
----- Original Message -----
From: Petr Jeřábek
To: amber.scripps.edu
Sent: Thursday, February 19, 2004 4:08 PM
Subject: Re: AMBER: LES
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
http://chemi.muni.cz/~rowan
----------------------------------------------------
----- Original Message -----
From: Carlos Simmerling
To: 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.
----- Original Message -----
From: Petr Jeřábek
To: amber.scripps.edu
Sent: Thursday, February 19, 2004 1:10 PM
Subject: AMBER: LES
dear amber users
I use the LES method for the protein (haloalkane dehalogenase about 300 aa) with small substrate(trichloropropane), but I dont have many experiences with LES running. I use these temperature parameters for
heatin phase:
&wt type='TEMP0', istep1=0, istep2=2500, value1=298.16,
value2=400.0,
&end
&wt type='TEMP0', istep1=2500, istep2=52500, value1=400.0,
value2=400.0
and these for cooling phase:
&wt type='TEMP0', istep1=0, istep2=80000, value1=400.,
value2=0.0
So, I would like to know if these temperature parameters are optimal for such system.
best regards
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
----------------------------------------------------
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Received on Thu Feb 19 2004 - 21:53:00 PST
