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 Thu, May 18, 2017 at 12:34 PM, Jake <jezerski.central.uh.edu> wrote: > Hello, > > I am trying to simulate a small 20 residue all atom peptide in implicit > solvent with a salt concentration of 150mM (saltcon=0.15). I have performed > these simulations using Generalized Born model and GBSA without any > problems in sander.MPI. I am now trying to use the same model with > Poisson-Boltzmann numerical calculations instead to improve my accuracy > (igb=10), but I get the following error message: > > "PBSA currently doesn't work with MPI inside SANDER" > > In my script I do not specify anything about surface area calculations. The > simulation works if I run non MPI sander, but it is significantly slower > and I will not be able to complete my simulations. > > Is there any way around this bug? Can I use GBSA or some approximation for > the surface area terms and PB numerical calculations for the electrostatics? > > Thanks. > _______________________________________________ > 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 Thu May 18 2017 - 14:30:03 PDT