AMBER Archive (2004)

Subject: Re: AMBER: Angle parameters in phosphate groups

From: David A. Case (case_at_scripps.edu)
Date: Sun Aug 15 2004 - 17:59:51 CDT

On Sat, Aug 14, 2004, Seongeun Yang wrote:
>
> I tried test simulations of ACE-SEP(-1)-NME and ACE-SEP(-2)-NME,

> I checked the structure, minimized by around 200 steps, to be unreasonble.
> The O-H and other O in the phosphage group stuck together and formed
> almost a triangle.

This is a common problem with simple force fields that are used to create
protonated phosphates. One way to "fix" this is to define a bond between P
and H, in order to keep the P-O-H angle fixed and prevent the type of
structure you are seeing. There is probably a better way, but exploring
things like this is probably required. Maybe one of the readers of this list
has some better ideas, or pointers to other people's experiences.

...good luck...dac

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