AMBER Archive (2008)

Subject: RE: AMBER: Input file for Minimization

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Sun Feb 10 2008 - 12:55:34 CST

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
Ross

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From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Campbell, Patrick
Sent: Saturday, February 09, 2008 13:19
To: amber_at_scripps.edu
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 min1.in file which he
quotes from the Simmerling, Strockbine and Roitberg paper could be modified
for this process.
 
min1.in
 
Stage1 - minimisation of TC5b
   & cntrl
       imin=1, maxcyc=1000, ncyc=500,
       cut=999., rgbmax=999., igb=1, ntb=0,
       ntpr=100
   /
 
If this file could be modified, could you suggest some parameters for this
process.
 
Thanks again for all your help.
 
Pat
 

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