AMBER Archive (2004)

Subject: Re: Re: AMBER: a question about Van der waals radius

From: Xiao He (hx_at_itcc.nju.edu.cn)
Date: Sat May 22 2004 - 08:55:05 CDT

  In my calculation of the interaction energy between a CYS residue of protein
and ligand of Nevirapine a HIV-1 RT drug). Since the van der waals radius
of the H linked to the S atom is 0.6A.While the distance between this H atom
with carbon atom in Nevirapine is 1.93A.
  The interaction energy is incompatible with the ab initio Gaussian result.
There's a strong repulsive reaction energy about 9 Kcal/mol using B3LYP/6-31G(d).
While using Amber7 it is around zero.
  Can we say it is a failure of force field?And the van der waals radius may be
a bit modified.
  Thanks for anyone's help!

He Xiao
 

>[ Charset GB2312 unsupported, skipping... ]
>
>These are just empirical parameters.
>real atoms are not spherical particles with some fixed and unambiguous radii.
>So the force fields are adjusted or optimized to reproduce some target
>data and it may well happen that some parameters in some parametrizations look
>"unphysical". Other parameters compensate for this (hopefully).
>Typically polar hydrogens appear to be "large" in some contacts
>and "small" (like been hidden inside the heteroatom) in others.
>Then the result of the parametrization may be as you notice and
>it is entirely OK for simulations.
>
>Best wishes Jiri Sponer
>
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¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡Xiao He
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡hx_at_itcc.nju.edu.cn
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2004-05-22

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