Re: [AMBER] Deformed structures

From: Damiano Spadoni <>
Date: Thu, 26 Nov 2015 11:44:38 +0000


the problem is exactly that one: the two hydrogens of the phosphate bend too much close one to each other leading to a move simulating rest of the structure that remains anchored to those fixed two atoms and so the deformation and instability.
If it's just a problem of charge I will try to change its own structure but I remember Gaussian didn't accept a -2 overall charge for that molecule leading to an optimized distorted structure.

From: David A Case []
Sent: 26 November 2015 00:27
To: AMBER Mailing List
Subject: Re: [AMBER] Deformed structures

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 Thu Nov 26 2015 - 04:00:04 PST
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