AMBER Archive (2002)

Subject: Fw: mm_pbsa

From: Lepsa (lepsik_at_marilyn.uochb.cas.cz)
Date: Fri May 24 2002 - 09:27:21 CDT

> Hi all,
> just a simplistic answer about GB and PB. PB is more rigorous so gives
more
> accurate results and takes more time to compute.
>
> Hope this helps.
>
> Martin.
> -------------------------------------------------------------------------- 

--
> --------------------------------------------------------------------------
--
> ----
> Martin Lepsik, PhD student            Phone:  +420/2/20183-540, Fax:
> +420/2/20183-292
> Dept. of Theor Chem & Center for Complex molecular Systems and
Biomolecules
> Institute of Organic Chemistry and Biochemistry (IOCB)
> Flemingovo nam 2,
> Czech Academy of Sciences,
> 166 10, Prague 6,
> Czech Rep.
> URL: www.uochb.cas.cz/~teochem
> ----- Original Message -----
> From: "X. Tan" <xjtan_at_u.washington.edu>
> To: <amber_at_heimdal.compchem.ucsf.edu>
> Sent: Tuesday, May 21, 2002 1:04 AM
> Subject: mm_pbsa
>
>
> >
> > Hi, It was my first attempt to use MM_PBSA. In MM_PBSA script, I
> > used GB program for solvation energy calculation, and my system includes
> > 207 res and about 300 wat(solvatecap). The belows is the result of
> > MM_PBSA.
> >
>
> --------------------------------------------------------------------------
> ----
> >                Complex (AB)           Receptor (A)            Ligand (B)
> >
Contribution ----------------------- ------------------------------------
> >           mean       std         mean       std         mean       std
>
> --------------------------------------------------------------------------
> > Eele  -7125.1719   19.5950   -7131.1970   19.4149      55.4103    1.7476
> > EvdW   709.6931  209.5975     725.9703  209.2015       6.5952    1.4115
> > Einter 2433.0899   20.8501    2403.6254   20.2172      29.4646    3.9879
> > Egas -3982.4187  209.1412   -4001.6013  208.8900      91.4594    4.0415
> > E(nonp)  54.3154    0.1371      54.7697    0.1353       3.5090    0.0209
> > E(nonpGB) 70.9311    0.1821      71.5346    0.1797       3.4393
0.0278
> > E(GB)  -1207.5667   16.0135   -1217.2146   15.9862     -22.1748
1.0877
> > E(sol) -1136.6355   15.9617   -1145.6799   15.9395     -18.7356
1.0818
> > E(GB+ele) -8332.7386  15.7243  -8348.4115  15.1948    33.2354  1.1136
> > E(tot,GB) -5119.0542  209.0189   -5147.2812  208.7454 72.7239    3.6919
> > ---------------------------------------------------------------------
> >              Interactions [AB-(A+B)]
> > ------------------------------------
> > Contribution       mean       std
> > ------------------------------------
> > Eelectrostat     -49.3852    4.5673
> > EvdW             -22.8723    4.2184
> > Egas             -72.2768    3.8228
> > E(nonpolar)       -3.9633    0.0399
> > E(nonpolGB)       -4.0428    0.0530
> > E(GB)             31.8228    2.5724
> > E(solvation)      27.7800    2.5821
> > E(GB+elect)      -17.5625    3.3003
> > E(total,GB)      -44.4969    2.8664
> > -----------------------------------
> >
> > Though there are a couple of emails on the list talking about meaning of
> > each items, I am still not clear what is the exact meaning for
> > the terms Egas and Einternal, and where them come from.
> >
> > Secondly, it looks weird that the std values of Evdw and Egas for
complex
> > and receptor are much larger than the others. Is there something wrong
> with my
> > computation?
> >
> > The last question is which program, delphi or GB generally gives better
> > solvation energy?
> >
> > Can anyone help me with those? Thanks a lots.
> >
> > Xiaojian Tan
> >
>