Re: [AMBER] Problem with Phenylphosphonic acid

From: Gustaf Olsson <>
Date: Sat, 20 Jul 2019 11:51:12 +0000

Hello David

As I am enjoying some days of work I will look into this as soon as I get back to the office. No, I am not using gaff2 though I will definitely give that a try and look into the angle constant to see what I can accomplish.

Thank you for you tips and have a nice weekend

// Gustaf

Från: David Case <>
Skickat: den 14 juli 2019 14:50:51
Till: AMBER Mailing List
Ämne: Re: [AMBER] Problem with Phenylphosphonic acid

On Fri, Jul 12, 2019, Gustaf Olsson wrote:
>I am running three different systems that contain pehnylphosdhonic acid,
>the neutral form (ppa) the anion (pp1) and the double negative anion

I bet that one of the protons on the phosphorous is getting very close
to one of the other phosphate oxygens. At least, this is a common
problem with protonated phosphates, although it's not clear why ppa
should be different than ppa1.

Are you using gaff2? One of the important changes between gaff and
gaff2 is that atom type "ho" is given non-zero van der Waals radii,
which should prevent the hydrogen from getting too close to a
neighboring oxygen. You may also need to increase (say double) the
P-O-H angle constant.

Since the problem happens quickly, run a short trajectory with ntwx=1 or
2, and visualize the geometry of the phopshate group as it gets close to
the point where the system crashes.

...hope this helps...problem could be something different, of

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