AMBER Archive (2000)

Subject: Re: Harmonic restraints on distances in sander

From: Andrea Bernini (andrea_at_neriserv.chim.unisi.it)
Date: Wed Mar 08 2000 - 10:37:09 CST

Vickie Tsui wrote:
>
> You could use distance restraints provided as part of the NMR refinement
> utilities to impose harmonic restraints on inter-atomic distances. Right
> now the penalty function is such that you can enter r1, r2, r3, r4 values.
> If R is the current distance, then the penalty function is:
>
> R < r1 linear
> r1 <= R < r2 parabolic
> r2 <= R < r3 Epenalty = 0
> r3 <= R < r4 parabolic
> r4 <= R linear
>
> If you want a purely harmonic function, set r1 to 0, r2=r3, and r4 to a
> large number, and that should work.
>
> vickie

Interesting, but in wich way is it possible to apply an harmonic
function to all bonds starting from a PDB file (without dg file) (I beg
aprdon if this is a trivial question)?

Thanks, Andrea.
___
Dr. Andrea Bernini, Ph.D.
Molecular Biology Dept.
University of Siena
Via Fiorentina 1, 53100 Siena, Italy
Phone +39 577 234911
Fax +39 577 234903