Re: ABF calculations

From: Jerome Henin (
Date: Mon Nov 19 2007 - 15:56:17 CST

If I were you, before starting such a calculation, I would get a feel
for the technical issues involved by trying to run a "small", "easy"
ABF calculation, such as the acetate-guanidinium ion pair that we
describe in the reference paper of NAMD's ABF implementation.

I don't think the "brute-force" approach will work here. In
particular, the orientational averaging would not work. It would
probably be possible to sample a particular dimerization pathway by
enforcing orientational restraints (see e.g. the acetate-guanidinium

Is the interaction *free energy* along a dimerization pathway really
what you are interested in? There should be means to estimate the
interaction energy in the dimer through "standard" simulations,
although I have never thought about the specifics. Anyway, that would
be easier to obtain and probably easier to interpret, as well.

On Nov 19, 2007 3:33 PM, jia <> wrote:
> Dear NAMD users and Jerome,
> I'm trying to use ABF method to calculate the binding energy of two small size
> proteins, 140 a.a for one and 57 for another, and I'm wondering if it's a good
> idea to choose the reaction coordinate as the distance separating the centers
> of mass of these two domains given the fact that many atoms will be
> participating to the center of mass. Any suggestions will be appreciated.
> Thanks much!
> Jiancong
> Postdoc Research fellow
> Center for Molecular Biophysics,
> Oak Ridge National Lab
> Oak Ridge, TN, 37830

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