Re: [AMBER] Adding a Dummy Atom to Benzene

From: Samuel Walpole (PHA) <"Samuel>
Date: Fri, 21 Oct 2016 12:36:16 +0000

Dear David,

I am trying to use a high concentration of benzene molecules to act as a probe for ligand binding sites on a protein of interest, following the methodology outlined in this paper:

In the paper they say that, in order to prevent aggregation of benzene molecules, they added " an additional massless particle to the geometric center of each benzene molecule" and set the Lennard-Jones parameters for interactions between these particles to Rmin = 24 A and = -0.01 kcal/mol.

Basically, I want to ensure that my benzene molecules do not aggregate during my simulations, so any advice on how this could be achieved, without affecting its interaction with the protein, would be appreciated.

Many thanks,

-----Original Message-----
From: David A Case []
Sent: 21 October 2016 13:19
To: AMBER Mailing List <>
Subject: Re: [AMBER] Adding a Dummy Atom to Benzene

On Thu, Oct 20, 2016, Samuel Walpole (PHA) wrote:

> Thank you for your reply. I've read that this can be achieved by
> considering the dummy atom as an 'extra point', such as the extra
> point in TIP4P water. How would I define my dummy atom as an extra
> point in leap? The documentation doesn't seem to go into this.

Amber supports only certain types of extra points, that are hard coded into the code (e.g. the define_frames() routine in extra_pts.F90 in sander.) You would have to grok this code (there are comments, but no formal documentation), then add a new section.

What are you trying to do with this point? Note that you can generate restraints (extra FF terms) that refer to the center of mass of the benzene ring. Maybe that will serve your needs(?)


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