RE: [AMBER] I do need your help, please

From: Ross Walker <>
Date: Thu, 8 Apr 2010 22:52:19 -0700

Hi William,

> Dear AMBERI know my questions may look silly, but I got confused, I did
> read lot of papers, emails and couldn't get a definite answer.PLEASE, I
> do need your help.1- Is extra point massless? The original paper says
> its mass is  3.00 and most of mail on amber list says it is massless.2-

My understanding of extra points is as follows - someone can correct me if I
am wrong here:

Extra points in AMBER 10 (not sure about previous implementations) are mass
less. They are 'fixed' to their host atom and they move entirely with this
atom. Forces on the extra points are propogated onto the 'host' atom and the
extra points position remains fixed relative to the host atom. You can
consider them as simply being off center charges.

> what is the difference between massless dummy atom
> and massless extra point in amber force field?

Dummy atoms are used in things like free energy perturbation calculations -
alchemical changes where an atom is made to disappear etc but the code is
written in such a way that it doesn't expect atoms to simply vanish. Hence
the need for a dummy atom. They are very different from extra points in that
extra points are specific off center charges added to certain atoms.

>3- why extra point has
> NONB EP       1.0       0.0? I see in some files, EP NONB values are
> 0.0 0.0 so which one is the correct value?

Extra points have no VDW radius and do not take part in VDW interactions.
They simply provide off center charges. This makes sense if you think about
it since they are designed to represent lone pairs on things like Oxygens.
The VDW radius of the underlying oxygen atom is assumed to encompass the off
center charge.

4- the distance between lone
> pair and Oxygen (for example) is 0.35. This is the distance between
> center of oxygen and center of lone pair, The problem is the VWD radius
> of oxygen is 1.52, does it mean it looks like a loop inside a sphere?

It looks like an additional point charge inside the VDW exclusion radius of
the oxygen. Since the extra points feature ONLY in the pairwise
electrostatic calculations so they have no effect on the VDW potential.

> so the dominant interaction should be with the oxygen. Sorry for any
> inconvenience caused by my email.Any kind of help would be
> appreciated.thanks in advance

The dominant interaction is between a lone pair and another charge. The lone
pair does Not have an electrostatic interaction with its host atom, or
indeed with any 1-2, 1-3 or 1-4 atoms. See $AMBERHOME/src/sander/extra_pts.f
for a description of this.

I hope that helps.

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | |

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Received on Thu Apr 08 2010 - 23:00:03 PDT
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