Dear Ray,
Thanks very much that you can give me an answer on Sunday. I am sorry for
not telling you that I used amber11 together with ambertools-1.5 to do the
calculation. For the parameters, I used the default ones in the first
calculation. That's the point confusing me, how can this happen? How can I
figure it out? Thanks very much!
Best Regards,
Qinghua
Ph.D. student
Juelich Research Center
On Sun, Nov 20, 2011 at 4:00 PM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:
> Dear Qinghua,
>
> For one thing, your PBSUR and GBSUR are already different -57.5 vs
> -9.7.Apparently you are using different parameters between the two
> models.
>
> Maybe I shall recommend using the latest Ambertool so it's easier to
> trace down your problem in the setup?
>
> All the best,
> Ray
>
> On Sun, Nov 20, 2011 at 12:10 AM, Qinghua Liao <fantasticqhl.gmail.com>
> wrote:
> > Dear amber users,
> >
> > I did a binding free energy of a ligand to a protein using mm_pbsa.pl,
> here
> > is the result:
> >
> > # DELTA
> > # -----------------------
> > # MEAN STD
> > # =======================
> > ELE -67.88 7.84
> > VDW -66.86 3.92
> > INT -0.00 0.00
> > GAS -134.74 8.89
> > PBSUR -57.52 1.98
> > PBCAL 115.17 9.15
> > PBSOL 57.64 9.07
> > PBELE 47.29 8.98
> > PBTOT -77.10 9.24
> > GBSUR -9.67 0.33
> > GB 160.07 21.87
> > GBSOL 150.40 21.87
> > GBELE 92.20 22.30
> > GBTOT 15.66 22.00
> >
> > I am wondering why PBTOT can be -77.10 while GBTOT be 15.66, I think it
> > does not make sense. So how should I explain such a situation? Thanks
> very
> > muc!
> > --
> > Best Regards,
> >
> > Qinghua
> > Ph.D. student
> > Juelich Research Center
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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Received on Sun Nov 20 2011 - 08:00:02 PST
