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-- Ray Luo, Ph.D. Professor, Biochemistry, Molecular Biophysics, and Biomedical Engineering University of California, Irvine, CA 92697-3900 On Fri, Jun 27, 2014 at 8:27 AM, JPB <jpb.q4md-forcefieldtools.org> wrote: > Dear users, > > I am performing free energy calculation with MMPBSA.py. > In one system with the Poisson Boltzmann model, > the van der Waals energy (VDWAALS) and the electrostatic > energy (EEL) are not taken into account. > In the FINAL_RESULTS_MMPBSA.dat file the lines devoted to > VDWAALS and EEL do not appear and it is also surprising > that for the ENPOLAR contribution "Std. Dev." > and "Sd. Err. of Mean" equal 0.00 > > In the _MMPBSA_complex_pb.mdout.i files, one can read: > eff.c(2829) enb --> 0.000 > eff.c(2830) eel --> 0.000 > eff.c(2831) e_pb --> 0.000 > > In the meantime in the same job these two contributions are computed > when using the generalized Born model. > > It seems that something somewhere turns off the computation of electrostatic > and van der Waals energies. > My system is an oligomer made of 12 molecular units. > I performed the same computations with oligomers of 1, 2, 4, 6, and 9 > molecular units and these two contributions were computed. > I don't know where to look for the origin of this problem with the 12-unit > system. > Any help is welcome. > > Cheers. > JPB. > > > _______________________________________________ > 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 Jun 27 2014 - 10:00:03 PDT