AMBER Archive (2006)

Subject: Re: AMBER: Values of Spring Constants

From: David A. Case (case_at_scripps.edu)
Date: Wed Feb 01 2006 - 10:38:13 CST

On Wed, Feb 01, 2006, Sai Kumar Ramadugu wrote:

> Actually I was trying to understand the functioning of Umbrella Smapling.
> For the same I took a protein of 40 aminoacids and did a GB simulation with
> restraints on phi angle of 2nd amino acid which is Alanine.
> My restraints input file is as follows:
> # 2 ALA PHI: (1 ASP C)-(2 ALA N)-(2 ALA CA)-(2 ALA C) 120.0 180.0
> &rst iat = 13, 15, 17, 23,
> r1 = 119.0, r2 = 120.0, r3 = 180.0, r4 = 181.0,
> rk2 = 2.0, rk3 = 2.0, &end

To use WHAM, you need to define a harmonic potential, where r2=r3 and r1 and
r4 are far away from r2 and r3, as described on page 138 of the Users' Manual.
The force constant will be twice the values you give for rk2=rk3 (because
Amber historically does not include a factor of 1/2 in these constraint
energies.)

...good luck...dac

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