AMBER Archive (2003)

Subject: Re: AMBER: Fxnal form of NMR-style restraints

From: Holger Gohlke (gohlke_at_scripps.edu)
Date: Thu Aug 28 2003 - 17:41:04 CDT

Kristina Furse wrote:
>
> Hi all-
>
> >From the AMBER 7 manual, in Sander section 4 describing the implementation of
> restraints (DISANG file) it says the following:
>
> r1 <= R < r2 Parabolic, with force constant k2. E=0 at R=r2.
> r2 <= R < r3 E=0.
> r3 <= R < r4 Parabolic, with force constant k3. E=0 at R=r3.
>
> Does this mean the "parabolic" part is of the form E=k(x-xi)**2, and not
> E=0.5k(x-x1)**2 harmonic oscillator?
>
> Any response or suggestion for where in the code to look this up would be
> greatly appreciated!

Have a look at the beginning of disnrg.f in $AMBERHOME/src/sander. The
parabolic part is calculated as E = ki*(r-ri)**2.

Best regards

Holger

>
> Kristina
>
> ****************************************************
> Kristina E. Furse
> Department of Chemistry
> Center for Structural Biology
> Vanderbilt University
> email: kfurse_at_structbio.vanderbilt.edu
>
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-- 
+++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Dept. of Molecular Biology, TPC15
The Scripps Research Institute
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La Jolla, CA 92037   USA
phone: +1-858-784-9788
fax:   +1-858-784-8896
email: gohlke_at_scripps.edu
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