Re: [AMBER] Deformed structures

From: David A Case <>
Date: Wed, 25 Nov 2015 17:27:29 -0700

On Wed, Nov 25, 2015, Damiano Spadoni wrote:
> I am try to run the heating step of a protein containing pyridoxal
> phosphate as cofactor.
> ...the mentioned pyridoxal structures appeared deformed, ....

There have been a lot of posts recently about the problems involved in
getting good force fields for phosphates. The origin of most of the problems
(not sure about your "deformations") is that a hydrogen atom on the phosphate
can interact with one of the other oxygens on the phosphate group, leading to
distorted geometries and instabilities if the hydrogen and oxygen get too

You can try some of these ideas, but make sure that you really need a
protonated phosphate: in many environments, this group will have a -2 charge,
and the problem mentioned above won't exist. (Assuming of course, that we are
talking about the same problem....)


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Received on Wed Nov 25 2015 - 16:30:03 PST
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