Re: [AMBER] Generating RESP Charges For Tightly-Bound Complexes - Charges from the complexes or the fragments?

From: David A Case <>
Date: Sun, 28 Jun 2015 08:09:52 -0400

On Sat, Jun 27, 2015, Damian G. Allis, Ph.D. wrote:
> In an example system, I’ve a family of cucurbit[N]uril (N =
> 5,6,7) cages containing a neutral para-carborane (C2B10H12). For
> the cucurbit[7]uril:para-carborane, the carborane cage sits with
> more-or-less van der Waals packing - the calculated charges for the
> isolated fragments and the full complex are very similar to one
> another. For the cucurbit[6]uril:para-carborane complex, the cage is
> quite tightly packed into the cururbituril (perhaps the pocket is too
> small for the cage experimentally, but that’s peripheral to the
> question).

The RESP method (or other methods that fit electrostatic potentials to points
exterior to the molecule) become pretty poorly determined when you have atoms
that are buried: many different charge combinations for such buried atoms
yield almost exactly the same external potential.

The "R" part of RESP regularizes this problem in an ad hoc but often useful
manner. But it is still the case that charges for atoms near the surface are
much better determined than are those far from the surface. It sounds like
you may be encountering this, especially for the complex.

This doesn't address the problem of what to do in your simulations. But that
depends (a lot) on other factors, like what you are trying to learn; how much
time you have to spend on this problem, and so on.


AMBER mailing list
Received on Sun Jun 28 2015 - 05:30:02 PDT
Custom Search