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

From: Ray Luo, Ph.D. <ray.luo.uci.edu>
Date: Mon, 2 Dec 2013 16:35:17 -0800

Yes. The next release will be called Amber14 ...

Ray

--
Ray Luo, Ph.D.
Professor,
Biochemistry, Molecular Biophysics, and
Biomedical Engineering
University of California, Irvine, CA 92697-3900
On Mon, Dec 2, 2013 at 3:52 PM, <psu4.uic.edu> wrote:
> 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 - 17:00:02 PST
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