AMBER Archive (2006)

Subject: Re: AMBER: MM-PBSA problem

From: Varsha Goyal (vgusp_at_yahoo.ca)
Date: Fri Dec 01 2006 - 15:35:27 CST

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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