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
>
>-----------------------------------------------------------------------
>The AMBER Mail Reflector
>To post, send mail to amber.scripps.edu
>To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
>__________ NOD32 1.770 (20040521) Information __________
>
>This message was checked by NOD32 Antivirus System.
>http://www.nod32.com
= = = = = = = = = = = = = = = = = = = =
致
礼！
Xiao He
hx.itcc.nju.edu.cn
2004-05-22
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sat May 22 2004 - 15:53:01 PDT
