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-- Ray Luo, Ph.D. Professor Biochemistry, Molecular Biophysics, Chemical Physics, Chemical and Biomedical Engineering University of California, Irvine, CA 92697-3900 On Mon, Mar 21, 2016 at 7:06 PM, Mary Varughese <maryvj1985.gmail.com> wrote: > Sir, > > Infact i have tried multiple trajectory approach also (10 ns trajectory). > But didnt get any favorable result. > > May be because i havent considered "make sure the average > delta G has converged by checking cumulative averages of all three > runs (complex, receptor, and ligand)". Would you please explain cumulative > average? > And also about entropy estimation. ? It would be really helpful. > > Thanking you for your time and reply > > mary > > > On Tue, Mar 22, 2016 at 6:09 AM, Ray Luo <rluo.uci.edu> wrote: > >> Hi Mary, >> >> If you have a flexible ligand, the single trajectory approach is >> probably not the best way to go. Please try the multi-trajectory >> approach. Apparently, a key point here is to make sure the average >> delta G has converged by checking cumulative averages of all three >> runs (complex, receptor, and ligand). However, some sort of entropy >> estimation is also important to take into account the conformational >> flexibility in the delta G calculation. >> >> All the best, >> Ray >> -- >> Ray Luo, Ph.D. >> Professor >> Biochemistry, Molecular Biophysics, Chemical Physics, >> Chemical and Biomedical Engineering >> University of California, Irvine, CA 92697-3900 >> >> >> On Fri, Mar 18, 2016 at 9:48 PM, Mary Varughese <maryvj1985.gmail.com> >> wrote: >> > sir, >> > >> > these are the files used to calculate PBTOT and entropy. I have done it >> > with other ligands(more rigid ligands) successfully. The problem here is >> > that the current ligand is half part flexible(a ch2-ch2-ch2-ch3 flexible >> > chain). Though the ligand bind experimentally and >> theoretically(throughout >> > the simulation time) the movement of the flexible region is causing >> changes >> > in PBTOT and entropy such that i cant get a statistically reliable value >> > (the final value obtained are highly positive; when i check the values >> (BE) >> > for each frame its deviating very much). The flexible part is causing >> that. >> > >> > So i would like to know which strategy i should be adopted in such cases. >> > >> > >> > thanking you for ur reply >> > >> > On Sat, Mar 19, 2016 at 6:43 AM, Ray Luo <rluo.uci.edu> wrote: >> > >> >> Mary, >> >> >> >> Maybe a bit more info is helpful, i.e. your inpu file. Also please note >> >> that mmpbsa single trajectory approach is more useful for delta delta G >> >> estimation. >> >> >> >> All the best, >> >> Ray >> >> On Mar 16, 2016 5:20 PM, "Mary Varughese" <maryvj1985.gmail.com> wrote: >> >> >> >> > Sir, >> >> > >> >> > I run some DNA-ligand1 complexes. Though the ligand remains bind >> >> throughout >> >> > the simulation, (the ligand binds experimentally also), I am not >> getting >> >> a >> >> > favorable binding energy from MMPBSA (single trajectory approach). The >> >> > ligand has a CH2-CH2-CH2 chain on one end which causes the ligand some >> >> > movement (entropy changes) and hence a stable binding energy is not >> >> > possible. Is there any other way to quantify the binding energy. Would >> >> you >> >> > please suggest a reliable approach in such situations where the ligand >> >> has >> >> > much flexibility? >> >> > >> >> > thanking you >> >> > mary >> >> > _______________________________________________ >> >> > 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 >> > _______________________________________________ > 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/amberReceived on Mon Mar 21 2016 - 23:30:04 PDT