Re: AMBER: 'ho' vDW parameters

From: Junmei Wang <>
Date: Mon, 8 Sep 2003 15:01:25 -0500

I think the vDW parameters of 'ho' was borrowed from parm94 force field
directly. I also found some minimized phosphates and sulfates are broken
using gaff.dat with a dielectric constant of 1 (gas phase) in our test of
the general amber force field (am1-bcc charge). However, if dielectric
constant of 4 (gas phase) was used, the failure vanished. Anyone knows why
vDW radius of "HO" is set to 0.0 in parm94?


Dr. Junmei Wang
Chemistry & Biophysics
Encysive Pharmaceuticals
7000 Fannin, Houston TX 77030
Tel: 713-5786649
Homepage: Http://

             "Lee, Matthew"
             Sent by: To
             owner-amber.scrip "''"
             09/05/2003 05:33 Subject
             PM AMBER: 'ho' vDW parameters
             Please respond to

I'm curious as to why the 'ho' vDW parameters in gaff.dat were set to mimic
the OPLS hydrogens, with 0.00 vDW radii.

I found, that in neutralized phosphates and sulfates, this can lead to
disastrous effects, since 1-3 VDW repulsons are ignored in AMBER between
two oh's, instead treated implicitly in the valence angle. If an 'ho' is
bumped close enough to its neighboring 'oh' (not the 'oh' that it is
covalently bound to), the attraction between 'oh' and 'ho' grows infinitely
large and causes LINMIN failures. This is because the oh-p5-oh angle term
is the only thing to deter this and maxes out at around +45 kcal/mol as
the ho-oh-p5, which provides for only 90 kcal/mol of repulsive energy.
quickly, the 'oh' and 'ho' can be superimposed on top of one another and
their infinite electrostatic interaction dominates the 90 kcal/mol of
repulsive angle terms.

   ho ho ho
  / / /
 oh oh -----> oh-ho|oh
  \ / | /
   \ / | /
    p5 p5

Since the vDW radius of oh is 1.721 and the bond distance between oh-ho is
0.96, a vDW radius for 'ho' of 0.6, like all the other h's in gaff.dat,
would still leave the 'ho' within the radius of the 'oh' *and* prevent the
atom superposition.

Is there a reason I missed for why the 'ho' radius should not be set to a
non-zero value?

I read a 1/2003 post by Case on the reflector discussin phosphates in
nucleic acid simulations, that talked about adding a covalent bond between
the P and the H. I can see that this would also help to deter the atom
superpositions and am wondering if that has any advantages over increasing
the vDW radius of the 'ho' to a non-zero value.


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Received on Mon Sep 08 2003 - 21:53:05 PDT
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