AMBER Archive (2006)

Subject: Re: AMBER: MM-PBSA problem

From: vanessa wai (wai.vanessa_at_gmail.com)
Date: Sat Dec 02 2006 - 03:08:15 CST

hi. I used Amber 8.

Any ideas?

Thanks,
Vanessa

On 12/2/06, Ray Luo <rluo_at_uci.edu> wrote:
>
> Which Amber distribution are you using?
>
>
>
> Ray
>
>
>
> -----Original Message-----
> *From:* owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] *On
> Behalf Of *vanessa wai
> *Sent:* Thursday, November 30, 2006 5:27 PM
> *To:* amber_at_scripps.edu
> *Subject:* AMBER: MM-PBSA problem
>
>
>
> 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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