AMBER Archive (2005)

Subject: AMBER: Position restraints and Models

From: Steve Seibold (seibold_at_chemistry.msu.edu)
Date: Thu Dec 01 2005 - 14:54:06 CST

Hello amber users

 

I have a homology model that passes all procheck evaluations and
Ramachandran analysis. However I have found that when I energy minimize
the protein, the structure is very sensitive to a sudden change in the
restraining force constant from 5 to 1 kcal/mol. I may be missing the
obvious here, but what I want to do is apply a Cartesian "position"
restraint (not distance between two atoms etc.) for all the atoms of my
protein using a harmonic force constant which changes its value
(continuously in small increments) over time through so many steps. Is
this possible in AMBER? May be it is just as well to minimize by
releasing the restraint from 5 to 4 to 3....to 1, running 1000
steps/unit change in restraint? If some one has experience in this area
I would greatly appreciate any advice.

 

Thanks, Steve

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