AMBER Archive (2008)

Subject: RE: AMBER: Gradual releasing of position restraints

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Nov 25 2008 - 10:48:13 CST

Hi Dmitri,

 

I question why you need the restraints at all here. Typically one just uses
restraints for situations where the initial structure has some instabilities
- i.e. it was a model built structure (such as in the DNA Tutorial B-1). If
you are starting from a crystal structure then a MM force field would have
been used to relax that structure, with some kind of x-ray restraints, and
so it should be fairly stable. So why not just do away with the restraints
altogether at the beginning and see what happens. I am always wary of using
restraints with constant pressure anyway, technically it should work but it
has always felt a little unphysical to me.

 

The nice thing about computational modeling is that if what you try doesn't
work and it explodes you can always go back and try again ;-).

 

Good luck,

Ross

 

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Dmitri Nilov
Sent: Tuesday, November 25, 2008 6:23 AM
To: amber_at_scripps.edu
Subject: AMBER: Gradual releasing of position restraints

 

Hello, my question is about equilibration of two chain protein at constant
pressure.

After energy minimization and gradual heating at constant volume I switch to

constant pressure simulation. And during 50ps density equilibration with 2.0
kcal/mol-A2 position restraints on protein,

structure of my protein seems to become compressed. This appears because of
my protein consists of two chains that become

closer to each other during box size decrease. After density equilibration I
release restraints completely

and strained interchain conformation leds to unfavorable large fluctuations
in protein.

So I suppose that problem could be partially resolved by gradual releasing
of position restraints.

I want to release restraints in several steps, for example:

step1: 50ps, 2.0 kcal/mol-A2 position restraints on protein.

step2: 50ps, 0.5 kcal/mol-A2 position restraints on protein.

step3: 50ps, 0.1 kcal/mol-A2 position restraints on protein.

step4: equilibration without restraints.

 

Could you advise me rational restraint values for each step? I know that 2.0
kcal/mol-A2 restraint rather strongly fix atoms at initial position

so I suppose this value is appropriate for first step. But what restraints
is appropriate for other steps?

 

Dmitri Nilov,

Lomonosov Moscow State University

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