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

From: Ray Luo, Ph.D. <ray.luo.uci.edu>
Date: Mon, 18 Nov 2013 16:09:12 -0800

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
>
> ÄGvdw
>
> ÄGelec
>
> *ÄGpb*
>
> *ÄGnon-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 - 16:30:02 PST
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