Custom Search
-- Ray Luo, Ph.D. Professor of Structural Biology/Biochemistry/Biophysics, Chemical Physics, Biomedical Engineering, and Chemical Engineering Department of Molecular Biology and Biochemistry University of California, Irvine, CA 92697-3900 On Fri, Jul 6, 2018 at 12:56 AM Charles Mariasoosai <charlesmariasoosai51.gmail.com> wrote: > > Dear Amber community, > there is a huge difference between the GB and PB energy values I have > calculated for the same trajectory > My system consists of protein-cofactor-inhibitor-4 zinc atoms. > I have treated Zn atoms in the cationic dummy atom method according to the > tutorial. > MD simulations are fine. > > IN MMPBSA calculation I treated "protein-cofactor-4 zinc atoms" as > "Receptor" and "Inhibitor" as "Ligand" > Initially, I have faced an error on PB calculation which I have solved with > "radiopt=0" flag. > > Later, MMPBSA calculations are also running smoothly. In the end, I saw > that the large energy difference in the calculated energy. > > my input file looks like this > ======================================= > |due GB and PB decomposition > |&general > | startframe=1, interval=1, verbose=1, > |/ > |&gb > | igb=5, saltcon=0.100, > |/ > |&pb > | istrng=0.100, radiopt=0, > |/ > |&decomp > | idecomp=1, > | dec_verbose=1, > |/ > *=======================================* > > > and, output file looks like this > > =================================================== > | > |Calculations performed using 5000 complex frames. > |Poisson Boltzmann calculations performed using internal PBSA solver in > sander. > | > |Generalized Born ESURF calculated using 'LCPO' surface areas > > > GENERALIZED BORN: > > Differences (Complex - Receptor - Ligand): > Energy Component Average Std. Dev. Std. Err. of > Mean > ------------------------------------------------------------------------------- > VDWAALS -46.3374 3.5124 > 0.0497 > EEL -257.7393 17.0368 > 0.2409 > EGB 271.0342 16.7361 > 0.2367 > ESURF -5.9403 0.3135 > 0.0044 > > DELTA G gas -304.0766 18.4957 > 0.2616 > DELTA G solv 265.0939 16.5853 > 0.2346 > > DELTA TOTAL -38.9828 5.8140 > 0.0822 > > > ------------------------------------------------------------------------------- > ------------------------------------------------------------------------------- > > POISSON BOLTZMANN: > Differences (Complex - Receptor - Ligand): > Energy Component Average Std. Dev. Std. Err. of > Mean > ------------------------------------------------------------------------------- > VDWAALS -46.3374 3.5124 > 0.0497 > EEL -257.7393 17.0368 > 0.2409 > EPB 277.7781 16.9461 > 0.2397 > ENPOLAR -33.2217 1.6110 > 0.0228 > EDISPER 53.4479 1.8152 > 0.0257 > > DELTA G gas -304.0766 18.4957 > 0.2616 > DELTA G solv 298.0043 17.0231 > 0.2407 > > DELTA TOTAL -6.0724 5.6593 > 0.0800 > > > ------------------------------------------------------------------------------- > ================================================= > > what is the reason for this, Is this because of I selected radii from > .prmtop itself for PB calculation? > If so how can I calculate reliable values? > Is there any other or alternate options? > > -- > > *-Regards-* > > *ம. ரம்ய சந்தர் சார்லஸ்(M.Ramya Chandar Charles*) > Research Scholar > c/o Dr. S. Mohane Coumar > Centre for Bioinformatics > Pondicherry university > Mob: +91-9283684619 > _______________________________________________ > 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 Fri Jul 06 2018 - 08:30:03 PDT