AMBER Archive (2008)

Subject: Re: AMBER: Leap atoms CL and OXT do not have a type

From: Bill Ross (
Date: Thu Oct 02 2008 - 12:36:58 CDT

> I am planning to get the radial distribution vs the distance between
> chloride ion and protein-atom which I know experimentally to be
> closest. This for all protein atoms in this situation. Using the vdw
> provided by Amber for chloride ion.

You might want to do it on a per-atom-type basis to disentangle
the effects.

> A point of my concern is that the protein atoms at issue are on amino
> acid side chains, in a couple of cases they belong to carboxylates
> that, as they come from leap, are not protonated. From the X-ray
> electron density map it is not entirely clear if, in such a case, it
> was CO2- or CO2H, and thus the interaction with Cl- is even less
> clear. Whether CO2- or CO2H depends on the pH the protein has sensed.

CO2H would be the more sensitive test I think - the more attraction
between Cl- and the molecule, the more sensitive it is to the vdw term.

> I am also organizing to measure pKa of the amino acids with software
> that, via monte carlo, explores the various conformational situations.
> Thus, at which stage should the radial distribution procedure be best
> carried out?

I would run simple dynamics (that's what I know :-). You might even consider
doing it with a simpler system if you can find an anion complex analogous to
the crown ether for cations.

On the other hand, your simulation may not be very sensitive to the
difference in Cl- radius involved here, especially since your solute
is not positively charged, although you would need to consider the
charges on the specific atoms in contact with the Cl-. Note that in
the paper I cited, the whole calculation turned on the contact between
the cation and the solute O's. (Also it happened that using uncorrected
ion vdw reproduced experimental results, so there was some cancellation
of errors that we could only hypothesize about.)

> Unless this question would require the Aladino's lamp.


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