AMBER Archive (2006)

Subject: Re: AMBER: SHAKE problem after minimization

From: Rachel (
Date: Thu Nov 23 2006 - 12:37:24 CST

Dear all,

Thanks very much for all your replies, after reading David's reply, I read
the information in amber manual about extra points, and looked at the files
for TIP4P and TIP5P water, I think it is a better idea to treat my 'dummy'
as the extra points. Thanks again for your good suggestion.

However, the information I have now seems to be not enough for me to
actually start to modify my hydrogen model. Can I ask where can I find more
details about the extra points?

I actually have copied my this email to Tom Darden, and really looking
forward to receiving your reply. Thanks in advance!

Best regards,

On 11/22/06, David A. Case <> wrote:
> > >
> > >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
> atoms.
> 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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