Re: amber-developers: Problem with SHAKE when icfe != 0

From: David A. Case <>
Date: Fri, 17 Mar 2006 12:21:57 -0700

On Thu, Mar 16, 2006, Ilyas Yildirim wrote:
> 4. When SHAKE is turned on (see ./ntc_2_ntf_2_icfe_1_ntb_1), the system
> blows up.

Have you read note (5) on p. 156 of the Users' Manual. Amber right now
a check that the *number* of shaken bonds is the same in both states, but
does not really check that the list of shaken bonds is identical (with
identical equilibrium bond lengths.) Patches to further validate the
files would be welcome.

> The reason why it does not work when SHAKE is turned ON is because of
> DH bonds. I think SHAKE is just constraining the H-bonds, not DH-bonds.
> DH-bonds are also like H-bonds, but the atom type for these dummy atoms
> are DH, not H or H?.

It uses the element type in LEaP (I think). So you would have to tell
that your dummy atoms are hydrogens. But using noshakemask would be a
solution. It would be great if you could try this (add noshakemask, with
ntc=2) since it has not been tested very much.


David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
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Received on Wed Apr 05 2006 - 23:49:37 PDT
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