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Ray Luo, Ph.D.
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
Office: (949)824-9528 Lab: (949)824-9562
Fax: (949)824-8551 e-mail: rluo.uci.edu
Home page: http://rayl0.bio.uci.edu/rayl/
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As Dave commented, the default carbon atom radii would cause
electrostatic solvation free energies in ff03ua to be a bit too
negative. For igb=5 applications with the mbondi2 radius set, the
recommended radii for all three united carbon atoms (C1, C2 and C3) are
2.2 A. The following is a summary on this study.
++++++++++++++++++++
We have compared both GB (igb=5) and PB (igb=10) with TIP3P with respect
to the reaction field energies (relative charging free energies between
in water and in vaccum) for 13 neutral amino acid sidechain analogs in
ff03aa and ff03ua. For both GB and PB, the modified Bondi radii was
assigned by "set default PBradii mbondi2" in tleap.
ff03AA:
GB(igb=5) PB (igb=10)
CC: 0.9960 0.9917
RMSD: 1.3346 1.1575
Slope: 1.1487 1.0849
Offset: -0.5310 -0.6333
ff03UA: (with the recommended radii 2.2A for the united carbons)
GB(igb=5) PB (igb=10)
CC: 0.9907 0.9885
RMSD: 1.1178 0.9115
Slope: 1.1275 1.0833
Offset: -0.2932 -0.2496
CC: correlation coefficient; RMSD, room-mean-squared deviation; Slope
and Offset are for linear regressions with respect to the TI reaction
field energies in TIP3P.
Note that we haven't tried to minimize RMSD for ff03ua with respect to
TI reaction field energies, but simply to make its regression slope
similar to that in ff03aa.
Received on Sun Nov 19 2006 - 06:07:13 PST