AMBER Archive (2004)

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

From: Jiri Sponer (sponer_at_ncbr.chemi.muni.cz)
Date: Sat May 22 2004 - 07:41:12 CDT

[ 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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