Dear Sofia,
I'm affraid there's no universal protocol for protein minimization.
Generally, you should do it stepwise, i.e.
minimize just 1) hydrogens 2) side chains 3) all atoms but C-alfa 4) all
atoms. All steps let's say 500-2000 steps. Last step until gradient 0.1 -
0.001, depends on your aim (dynamics or normal modes, respectively).
Your resulting structure will deviate but the question is how much.
Deviation of backbone atoms by 0.4-0.8 is O.K. You should examine your final
structure to check for abnormalities.
Also check AMBER tutorial pages!!
Good luck.
Martin Lepsik
----- Original Message -----
From: "m.elizabeth sophia" <mesophia_at_niper.ac.in>
To: <amber_at_heimdal.compchem.ucsf.edu>
Sent: Tuesday, September 03, 2002 6:01 PM
Subject: protein minimization
> We are doing some docking studies. Is there a common method for
> minimizing the
> protein structures. In my case the structures of proteins after
> minimization,
> seem to deviate from the original structure. Please assist.
> Sophia
Received on Mon Sep 02 2002 - 23:13:54 PDT
