AMBER Archive (2002)

Subject: Re: protein minimization

From: Lepsa (lepsik_at_marilyn.uochb.cas.cz)
Date: Tue Sep 03 2002 - 01:13:54 CDT

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