AMBER Archive (2006)

Subject: Re: AMBER: Values of Spring Constants

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Wed Feb 01 2006 - 07:05:14 CST

Sai Kumar Ramadugu wrote:
> Dear All,
> I wanted to do a simulation using the Umbrella Sampling. For restraints I
> was using the Phi torsional angle of a residue. As it was mentioned in AMBER
> manual to use WHAM to generated the potential of mean force, I used WHAM.
> But in the WHAM program it asks for the values of the spring (foce) constant
> for the restraining potential. How can I get the value of the spring
> constant for the Phi angle between N-C-CA-N. I looked at the parm99.dat file
> but there were four columns for the torsinal angles. Now which one among
> them could be the values of force constant? Please help me in this regard.
> Thanks and regards,
> Sai
>
The value of the restraint constant needed for umbrella sampling and
WHAM is NOT the one in parm99, but the one you yourself set in your
restraint file, assuming you had one.

Cheers
adrian 

-- 
                            Dr. Adrian E. Roitberg
                              Associate Professor
               Quantum Theory Project and Department of Chemistry

University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email adrian_at_qtp.ufl.edu
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