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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 Wed, Oct 12, 2016 at 10:03 AM, Vlad Cojocaru <vlad.cojocaru.mpi-muenster.mpg.de> wrote: > Thanks Ray for the tip...I will try with frcopt=5 ..... frcopt=0 is not allowed with eneopt=4 at the moment ... What does 5 do ? > > Best > Vlad > > On October 12, 2016 5:32:36 PM GMT+02:00, Ray Luo <rluo.uci.edu> wrote: >>Hi Vlad, >> >>Okay this is because the entry was not updated in the manual. Please >>check the keyword combination in the test case for pb_np3m. The frcopt >>should be 5 to match the eneopt=4. However, I think it should also >>allow users to set frcopt=0, even if force is always computed. >> >>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 Wed, Oct 12, 2016 at 7:44 AM, Vlad Cojocaru >><vlad.cojocaru.mpi-muenster.mpg.de> wrote: >>> Dear Ray, Dear all, >>> >>> Using non linear Poisson Boltzmann, I thought of trying the option >>> eneopt=4. However I always get the error: "PB Bomb in pb_read(): >>> combination of eneopt and frcopt is unsupported". I tried all >>possible >>> values for frcopt option (0,1,2,3) and also I tried an input without >>> defining frcopt at all (see below) but everytime the same error. Is >>the >>> "eneopt=4" option usable whatsoever ? >>> >>> Thanks for answering >>> >>> Best wishes >>> Vlad >>> >>> >>> >>> MMPBSA, Nonlinear PB, inp=2, sasopt=2 >>> &cntrl >>> nsnb=99999, dec_verbose=0, ioutfm=1, >>> ipb=2, ntb=0, cut=999.0, imin=5, >>> igb=10, inp=2, >>> / >>> &pb >>> epsin=4, epsout=80, smoothopt=1, >>> istrng=100.0, pbtemp=300, radiopt=1, >>> dprob=1.4, iprob=2.0, sasopt=2, saopt=0, >>> triopt=1, arcres=0.25, >>> npbopt=1, solvopt=1, accept=0.001, >>> maxitn=100, fillratio=4.0, space=0.5, >>> nbuffer=0, nfocus=2, fscale=8, npbgrid=1, >>> bcopt=5, eneopt=4, scalec=0, >>> cutfd=5.0, cutnb=15, nsnba=1, >>> phiout=0, npbverb=1, >>> decompopt=2, use_rmin=1, sprob=0.557, vprob=1.3, >>> rhow_effect=1.129, use_sav=1, >>> cavity_surften=0.0378, cavity_offset=-0.5692, >>> maxsph=400, >>> / >>> >>> -- >>> Dr. Vlad Cojocaru >>> Computational Structural Biology Laboratory >>> Department of Cell and Developmental Biology >>> Max Planck Institute for Molecular Biomedicine >>> Röntgenstrasse 20, 48149 Münster, Germany >>> Tel: +49-251-70365-324; Fax: +49-251-70365-399 >>> Email: vlad.cojocaru[at]mpi-muenster.mpg.de >>> http://www.mpi-muenster.mpg.de/43241/cojocaru >>> >>> >>> _______________________________________________ >>> 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 > > -- > Sent from my Android device with K-9 Mail. Please excuse my brevity. > _______________________________________________ > 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 Wed Oct 12 2016 - 12:00:02 PDT