Re: amber-developers: The UA radii revision to leap

From: Ray Luo <>
Date: Wed, 15 Nov 2006 11:04:01 -0800

Hi Dave,

Here is Chuck's last email on this.


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:
Home page:
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.
            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
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