AMBER: vdw of h atoms

From: Gustavo Pierdominici Sottile <>
Date: Fri, 28 Oct 2005 16:16:10 -0300

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

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Received on Fri Oct 28 2005 - 20:53:01 PDT
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