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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Nov 20 2011 - 07:30:03 PST
