AMBER Archive (2008)

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

From: Bill Ross (
Date: Thu Oct 02 2008 - 15:09:53 CDT

>> 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.
> That is interesting, also because my protein is quite large. On the
> fly, I remember of large azacrowns. In protonated form they complex
> chloride ions, if I remember a couple of anions, one above and one
> below the mean plane of the azacrown. X-ray diffraction data perhaps
> exist. However, this would involve the gaff force field alone. Could
> you imagine how to set up a periodic system for that, and would it be
> representative? Actually, with my protein complex there is also amino
> acid N (LYS) close to chloride.

Ideally you would want a complex with the same atom types as are in
contact in the protein. The system could be solvated to run with normal
pressure/density. Given the need for gaff, you might want to just run a
bit with the system you have and get the radial distribution of all solute
atom types around the ion to see how close the closest atom approaches
(the inner edge of what might be a broad first peak), then consider whether
it is reasonable. In our study it was easy because the contacting atoms
were O's, so we could use ion-O neutron diffraction data from water (come
to think of it, I wonder if that was a valid choice for ion-carbonyl_O

As I mentioned before, the difference may not be big enough to matter to
your simulation. Another way to approach it would be to guess at a smaller
radius and run your calculations both ways to see if there is a difference;
however to really 'prove' it, multiple long trajectories would need to be
run with different starting conditions with each radius, so this could be
expensive. Yet another approach could be to do some energy minimizations
to find which atoms the Cl- contacts, then do quantum calculations with
representative smaller molecules to see how big the differences are.

Given all this, the appropriate approach may be to collect expert opinions.
Reviewers may be content with the standard parameters.

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