Re: [AMBER] PARSE radii and effective radii IN MM/PBSA & MM/GBSA

From: <psu4.uic.edu>
Date: Mon, 2 Dec 2013 17:52:40 -0600

Dear Professor Luo,

   Thanks for your explanation. Will look forward the next Amber 14(?!).

   Henry


On Mon, Nov 18, 2013 at 6:09 PM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:

> Henry,
>
> MMPBSA actually uses the radii values in the prmtop files when
> INP=1/radiopt=0. These are mbondi or mbondi2 radii. They are similar
> to parse radii, but not the same, particularly those for the hydrogen
> atoms. PBSA will support the pqr format in the next year's release.
> When the new version is ready, you can use whatever radii in your pqr
> files.
>
> Ray
> --
> Ray Luo, Ph.D.
> Professor,
> Biochemistry, Molecular Biophysics, and
> Biomedical Engineering
> University of California, Irvine, CA 92697-3900
>
>
> On Mon, Nov 18, 2013 at 3:50 PM, <psu4.uic.edu> wrote:
> > 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
> >
> > ─Gvdw
> >
> > ─Gelec
> >
> > *─Gpb*
> >
> > *─Gnon-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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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>



-- 
Pin-Chih Su (Henry Su)
Ph.D. canditate
Center for Pharmaceutical Biotechnology (MC 870)
College of Pharmacy, University of Illinois at Chicago
900 South Ashland Avenue, Room 1052
Chicago, IL 60607-7173
office      312-996-5388
fax         312-413-9303
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Received on Mon Dec 02 2013 - 16:00:02 PST
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