AMBER Archive (2006)

Subject: Re: AMBER: SHAKE problem after minimization

From: David A. Case (
Date: Wed Nov 22 2006 - 16:24:44 CST

> >
> >Thanks for your reply, yes, i do have some home-made residues, which are
> >hydrogen molecules, i used a three-atom model, with two hydrogen atoms
> >(type HD) and one dummy atom in-between the two hydrogen atoms (type DH)

This sort of description for hydrogen molecules really ought to use the
"extra point" capability in sander, and not try to use SHAKE or light masses,
etc. This is how the extra points in TIP4P or TIP5P are handled, as well as
the "lone pair" extra points in ff02EP. The positions of these points are
updated on the fly, based on the coordinates of the "real atoms", and all
forces on these points are converted to the equivalent forces on the real

The types of dummy atoms that are allowed in Amber are hard-wired into the
code, in the define_frames() routine in extra_pts.f. If you name your real
hydrogen atoms in a way that makes the code think they are "heavy" atoms, name
the dummy atom starting with "EP", and define a bond from the extra point to
each one of these real hdyrogen atoms, I think(!) the code will recognize what
to do. But you will have to be prepared to study the code to see how extra
points are handled, and to experiment with your residue definitions to make
sure that everything is being done correctly. It will probably require adding
some debugging print statements in extra_pts.f to be sure that what you want
is really taking place. But as I read the code, what you probably want is
what the code calls an "ordinary" extra point.

Tom Darden is the person who wrote all of this, and may have some better
ideas, or some examples you could start from.

...good luck...dac

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