AMBER Archive (2006)

Subject: Re: AMBER: Values of Spring Constants

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Wed Feb 01 2006 - 06:52:50 CST

this is not supposed to be the values from the parm99.dat
file, it is the value of the harmonic force that YOU added
for the umbrella potential. it's hard to say more since you
didn't give any detail, or your sander input, etc.

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
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