Re: Harmonic restraints on distances in sander

From: Vickie Tsui <>
Date: Wed 8 Mar 2000 10:06:41 -0800 (PST)

> 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)?

Because the restraints input into AMBER are specified by the atom numbers
(see section 4 of Sander), you can write a simple script that will go down
the PDB file, take the atom numbers corresponding to the atom pairs for
which you'd like distance restraints from the PDB file (that would give
you the "IAT" variables). You can also calculate the distance between
those atoms from the coordinates in the PDB file, and that would determine
your "r2" and "r3" variables. Then the script can output those
information (plus your desired r1, r4, and force constants) out in the
format used for AMBER input restraints. You can do this for all atom
pairs if you choose (that will give you a huge amount of restraints,
depending on the size of your system), or for specified groups of the


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On Wed, 8 Mar 2000, Andrea Bernini wrote:

> 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
Received on Wed Mar 08 2000 - 10:06:41 PST
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