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-- Best Regards, Qinghua Ph.D. student Juelich Research Center On Mon, Nov 21, 2011 at 7:08 PM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote: > Qinghua, > > Can you stay with Ambertools and use the python script? It has more > control of input and the default is to set PB and GB calculations with > the same input parameters. > > All the best, > Ray > > On Sun, Nov 20, 2011 at 7:34 AM, Qinghua Liao <fantasticqhl.gmail.com> > wrote: > > 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 > >> > _______________________________________________ > >> > 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 > >> > > _______________________________________________ > > 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 > -- Best Regards, Qinghua Ph.D. student Juelich Research Center _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Mon Nov 21 2011 - 23:30:03 PST