AMBER Archive (2006)

Subject: Re: AMBER: MM-PBSA problem

From: vanessa wai (wai.vanessa_at_gmail.com)
Date: Sat Dec 02 2006 - 03:11:18 CST

Hi.

Thanks for that idea, I have stripped off all ions and water molecules prior
running MM-PBSA calculation, therefore I don't think free ions are the
reasons. Anyway, thanks a lot.

Regards,
Vanessa

On 12/2/06, Varsha Goyal <vgusp_at_yahoo.ca> wrote:
>
> Dear Venessa,
> I also had similar kind of problem in past, but in my
> case I have an Zn ion and PB is not very good in
> dealing with ions.
> Other thing was ion was free floating (not bound to
> anything), therefore during calculation surface is
> changing all the time which also gives huge error.
> I hope this help. Or you may want to read papers about
> how PB works
> Thanks
>
>
> --- vanessa wai <wai.vanessa_at_gmail.com> wrote:
>
> > Dear Amber users,
> >
> > Hello there. I encounter a problem in interpreting
> > the results that I got
> > from MM-PBSA calculation on binding free energy of
> > ligand to my protein.
> > PBTOT that I got (please refer below) from the
> > calculation is very very
> > positive (almost impossible), however GBTOT values
> > looks like a more
> > acceptable value as compared to experimental value.
> > Any ideas on how this
> > could happen? Any ideas are welcome.
> >
> > Thanks a lot and hope to hear from you all soon.
> >
> >
> > # DELTA
> > # -----------------------
> > # MEAN STD
> > # =======================
> > ELE - 5.72 16.86
> > VDW -87.34 11.22
> > INT 0.00 0.00
> > GAS -93.06 13.61
> > PBSUR -7.00 0.20
> > PBCAL 718.76 210.20
> > PBSOL 711.76 210.01
> > PBELE 713.04 222.37
> > PBTOT 618.70 215.23
> > GBSUR -10.08 0.29
> > GB 81.72 13.44
> > GBSOL 71.64 13.63
> > GBELE 76.00 5.44
> > GBTOT -21.41 11.30
> >
> >
> > Best regards,
> > Vanessa
> >
>
>
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