Re: AMBER: vdw of h atoms

From: Jiri Sponer <>
Date: Fri, 28 Oct 2005 22:00:19 +0200 (MEST)

Dear Gustavo,

    if I understand properly, you work with a nonneutral
    system, correct? Then you can have large polarization
    term of several kcal/mol missing in the gas phase
    pair additive force field evaluation. To adjust the hydrogen
    "size", you would need to calculate the energy(distance) curve
    with a special emphasize to the short range repulsion region.
    It is not clear from your message whether you subtracted
    BSSE and how did you treat monomer deformation term.
    DFT itself is usualy not sufficient for benchmarking.


> Dear list: I am analyzing vdw interaction between CH3-NH3+ and water. The
> distance between one H atom of the methyl group and the oxygen atom of
> water is 2.15.
> The intermolecular energy is -12.0 kcal/mol obtained from gaussian using
> b3lyp 6-31g*. Using the force field (considering the H atoms of the methyl
> group as H3) gives an intermolecular energy of -7.9 kcal/mol. Knowing the
> problem of transferability of the vdw parameters of the hydrogen atoms, I
> decided to reduce the R value due to presence of a strong electron
> withdrawing group attached to the methyl group.
> I had reduced the R until 0.47(original value 1.187) and found that the
> intermolecular energy is -10.5 kcal/mol, and smaller values of R did not
> improve the value of the energy. So I decided to increase the e value of
> this H atom. The original value was 0.0157. Rising this value to 0.8, made a
> change in the energy of only 0.2 kcal/mol.
> After all that, I used a program that fits this two values (r and e) so
> as to reproduce the intermolecular energy. The values obtained were r=0.4093
> and e=1.79. I think that the r value is OK considering that H atoms do not
> have inner shell, and in this case, this value is strongly influenced by
> group attached to the carbon atom. What is surprisng is that the e value is
> more than two orders of magnitude bigger than the original one. I tried
> other configurations using the adjusted values and the ab initio energy
> could be reproduced.
> Does someone know why these values of r and e differ so much from the values
> present in the force field?
> Thanking in advance
> Gustavo
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Fri Oct 28 2005 - 22:53:01 PDT
Custom Search