AMBER Archive (2008)

Subject: RE: AMBER: Input file for Minimization

From: Campbell, Patrick (
Date: Tue Feb 12 2008 - 11:43:34 CST

Hello Dr. Walker,
Thanks for your prompt and precise response to my questions!
I apologise for not being too explicit in my initial explanation - allow me to try again.
I would like to examine the 'most stable' conformation of the 300aa protein based solely on its aa sequence - currently, it has no PDB file.
Towards this end, I would employ minimization before MD to ultimately obtain the stable folding pattern of the protein in two states - in vacuo and solvated in water. My understanding is that I will have to do the minimization (to clean up the structure) before the MD - (the MD employs both heating and equilibration of the structure as per files and shown below). At the end of the day, I would like to simulate binding interactions that exist between this protein and some selected ligands.
My question is this:
Following on your suggestion on explicit solvent environment, simulated annealing and cooling down to zero K, could you point me as to where I can obtain information (or the script itself) or the parameters for this simulation as it relates to the minimization, heating and equilibration steps? I am fairly new to AMBER and have not fully exhausted all of the reading material on the topic.
Thank you so much for all your help Dr. Walker and do have a great day!
Stage 2 equilibration 1 0-5ns
  imin=0, irest=1, ntx=5,
  nstlim=2500000, dt=0.002,
  ntc=2, ntf=2,
  ntt=1, tautp=0.5,
  tempi=325.0, temp0=325.0,
  ntpr=500, ntwx=500,
  ntb=0, igb=1,
Stage 1 heating of TC5b 0 to 50K
  imin=0, irest=0, ntx=1,
  nstlim=10000, dt=0.0005,
  ntc=2, ntf=2,
  ntt=1, tautp=1.0,
  tempi=0.0, temp0=50.0,
  ntpr=50, ntwx=50,
  ntb=0, igb=1,

From: on behalf of Ross Walker
Sent: Sun 2/10/2008 12:55 PM
Subject: RE: AMBER: Input file for Minimization

Hi Patrick,
This really depends on what you mean by the term minimize and what you want to do with the resulting structure. Note the file below will certainly minimized your structure (in implicit solvent) however it will only take you to the nearest local minimum which will mean you won't get much change in structure. If you want to explore more of the local phase space then you can try simple simulated annealing and then cooling down to zero K. Beyond that you will have to start looking in to procedures like replica exchange or other more complex approaches.
The minimization from the tutorial you are referring to was purely to "clean up" the structure prior to running molecular dynamics on the system.
Also note that a 200aa protein in explicit solvent is going to be very slow, you are probably better doing things in explicit solvent.
All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
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        From: [] On Behalf Of Campbell, Patrick
        Sent: Saturday, February 09, 2008 13:19
        Subject: AMBER: Input file for Minimization
        Hello All,
        I would like some information concerning the parameters to set for a minimization of a 200 aa, 30 kD protein. I was following from the AMBER tutorial by Ross Walker, and was wondering if the file which he quotes from the Simmerling, Strockbine and Roitberg paper could be modified for this process.
        Stage1 - minimisation of TC5b
           & cntrl
               imin=1, maxcyc=1000, ncyc=500,
               cut=999., rgbmax=999., igb=1, ntb=0,
        If this file could be modified, could you suggest some parameters for this process.
        Thanks again for all your help.

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