Dear Amber,
After reading the PARSE radii paper (J . Phys. Chem. 1994,98, 1978-1988),
some other related papers, and previous mailing lists, (
http://archive.ambermd.org/201208/0085.html,
http://archive.ambermd.org/201308/0044.html ,
http://archive.ambermd.org/201006/0531.html,
http://archive.ambermd.org/200704/0071.html,
http://archive.ambermd.org/201007/0594.html,
http://archive.ambermd.org/201006/0132.html ), we are still a bit confused.
MM/PBSA: According to the MMPBSA.py manual, if inp=1 and radiopt=0, it
seems like MMPBSA.py uses PARSE radii for the non-polar solvation energy
terms. However, a simple test in MM/PBSA using different prmtop in
various effective radii (bondi, mbondi, mbondi2) gives a slightly different
non-polar energy values. Is it because inp=1 and radiopt =0 forces
MMPBSA.py to overwrite effective radii (bondi, mbondi, mbondi2) over PARSE
radii?
MM/PBSA test results: 250 ps, inp=1, radiopt=0,
Bondi
ΔGvdw
ΔGelec
*ΔGpb*
*ΔGnon-polar*
bondi
-35.15
-15.15
*30.20*
*-2.3989*
mbondi
-35.15
-15.15
*32.38*
*-2.4313*
mbondi2
-35.15
-15.15
*30.12*
*-2.3972*
In MM/GBSA in MMPBSA.py, different effective radii settings (bondi, mbondi,
mbondi2) will affect dG(GB) for sure, as reported by various literatures
(igb =1,2,5,7,8 original publications). However, unlike the scenario in
MM/PBSA, wonder why Amber default settings force MM/GBSA non-sensitive to
the non-polar term (deltaGNPOLAR)?
MM/GBSA test results, 250 ps
Bondi
deltaGVDW
deltaGelec
*deltaGPBb*
*deltaGNPOLAR*
deltaGsolvation
deltaGBinding
bondi
-35.1465
-15.1476
*20.5781*
*-4.4684*
16.1097
-34.1844
mbondi
-35.1465
-15.1476
*22.5793*
*-4.4684*
18.1109
-32.1832
mbondi2
-35.1465
-15.1476
*19.961*
*-4.4684*
15.4926
-34.8015
Cheers,
Henry
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Received on Mon Nov 18 2013 - 16:00:03 PST
