AMBER Archive (2006)

Subject: RE: AMBER: SHAKE problem after minimization

From: Hayden Eastwood (
Date: Wed Nov 22 2006 - 13:13:24 CST

Dear Rachel

I have had similar problems to you when running dynamics with home-made
residues. There is a defect in the amber force field with regards to
treating various highly charged groups in bonding proximity. If you have a
home made molecule then I have the following question:

Do you have any Phosphate-oxygen bonding neighbours with very large opposite
charges? Or any other bonding pairs with huge charge differences? If you do,
this could be the cause of the crash. AMBER assumes that the bond angle
barrier is large enough to prevent neighbouring connected atoms from
collapsing into one another. However, in some situations (i.e. with
oppositely highly-charged atom pairs) this barrier is overcome and the atoms
are pulled down a pairwise electrostatic interaction slope until they
overlap and cause your energy to go crazy.

The cure: artificially increase the bond angle force constants in the force
field parameter file and this should prevent them running into each other
(although the dynamical behaviour of some of the affected groups will of
course be "stiffer").

I don't really understand the nuts and bolts of why the atoms descend into
one another given that there should be van der waals terms that prevent
this...Mike Crowley personally explained it to me once and whilst it made
sense at the time the explanation now seems a little fuzzy!

If it's not a home made residue with the above mentioned characteristics
then I'd suggest you follow Ross's advice.



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