Re: AMBER: SHAKE error

From: David A. Case <>
Date: Fri, 22 Jul 2005 13:46:42 -0700

On Fri, Jul 22, 2005, Agata Jurkiewicz wrote:
> Thank you for the hints.

I'm wondering now if there is not some problem with the force field. You
said originally that the molecule was dUMP. How did you make this? Are
there any protons on the phosphate?

I'm just making a guess here: we had problems with terminal phophates, where
the geometry could get quite distorted (leading to shake errors) with
"standard parameters". So, you might look closely at the phosphate

If this guess is correct, you shold see problems even with a vacuum simulation
with no waters. Of course, I am stretching here, but it would be good to know
if there is anything non-standard about your molecule.


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Received on Fri Jul 22 2005 - 21:53:01 PDT
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