AMBER Archive (2004)

Subject: Re: AMBER: LES

From: Petr Jeřábek (rowan_at_chemi.muni.cz)
Date: Thu Feb 19 2004 - 15:08:38 CST

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
   http://chemi.muni.cz/~rowan
 ----------------------------------------------------

  ----- Original Message -----
  From: Carlos Simmerling
  To: 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.
   
  ----- Original Message -----
    From: Petr Jeřábek
    To: amber_at_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_at_chemi.muni.cz
       http://chemi.muni.cz/~rowan
     ----------------------------------------------------

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