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-- Ray Luo, Ph.D. Professor, Biochemistry, Molecular Biophysics, and Biomedical Engineering University of California, Irvine, CA 92697-3900 On Fri, Oct 25, 2013 at 11:18 AM, Vlad Cojocaru <vlad.cojocaru.mpi-muenster.mpg.de> wrote: > Yes, but cutnb=0 is not acceptable for eneopt=1 .... > > Vlad > > > On 10/25/2013 07:52 PM, Ray Luo, Ph.D. wrote: >> Yes, for nonlinear PB, you have to live with eneopt=1 ... The default >> cutnb = 0 means no cutoff is used. >> >> Ray >> -- >> Ray Luo, Ph.D. >> Professor, >> Biochemistry, Molecular Biophysics, and >> Biomedical Engineering >> University of California, Irvine, CA 92697-3900 >> >> >> On Fri, Oct 25, 2013 at 10:08 AM, Vlad Cojocaru >> <vlad.cojocaru.mpi-muenster.mpg.de> wrote: >>> Thanks Ray, >>> >>> Yes ... I figured that out ... >>> >>> Maybe one last question ... The eneopt error came from using the >>> non-linear PB which appears incompatible with eneopt=2. >>> >>> What are the eneopt and cutnb recommendations for non-linear PB ? Would >>> eneopt=1 and cutnb=12 be acceptable or outrageous ? >>> >>> Thanks again >>> Vlad >>> >>> On 10/25/2013 06:56 PM, Ray Luo, Ph.D. wrote: >>>> Vlad, >>>> >>>> The python and perl scripts only accept a very limited set of options >>>> for PBSA. To test with all the options, you have to use PBSA program >>>> directly. Its user interface is like the SANDER program. >>>> >>>> All the best, >>>> Ray >>>> -- >>>> Ray Luo, Ph.D. >>>> Professor, >>>> Biochemistry, Molecular Biophysics, and >>>> Biomedical Engineering >>>> University of California, Irvine, CA 92697-3900 >>>> >>>> >>>> On Fri, Oct 25, 2013 at 9:02 AM, Vlad Cojocaru >>>> <vlad.cojocaru.mpi-muenster.mpg.de> wrote: >>>>> Dear all, >>>>> >>>>> When using mmpbsa_py_energy in MMPBSA.py and trying to change PBSA >>>>> options in _MMPBSA_pb.mdin, I get lots of weird errors. >>>>> Several options listed as PBSA options in the manual (e.g. ipb, sasopt, >>>>> triopt) are not accepted. Also when I specifically set eneopt = 2 in the >>>>> _MMPBSA_pb.mdin file, the calculation exists with an error saying that >>>>> eneopt = 1 requires a non-zero cutnb as if the input is not read correctly. >>>>> >>>>> I guess given all these problems with mmpbsa_py_energy, it is >>>>> recommended to use sander (by setting use_sander=1) >>>>> >>>>> Best >>>>> Vlad >>>>> >>>>> -- >>>>> Dr. Vlad Cojocaru >>>>> Max Planck Institute for Molecular Biomedicine >>>>> Department of Cell and Developmental Biology >>>>> 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/research/teams/groups/rgcojocaru >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> >>>> >>> -- >>> Dr. Vlad Cojocaru >>> Max Planck Institute for Molecular Biomedicine >>> Department of Cell and Developmental Biology >>> Röntgenstrasse 20, 48149 Münster, Germany >>> Tel: +49-251-70365-324; Fax: +49-251-70365-399 >>> Email: vlad.cojocaru[at]mpi-muenster.mpg.de >>> >>> >>> _______________________________________________ >>> 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 >> >> > > -- > Dr. Vlad Cojocaru > Max Planck Institute for Molecular Biomedicine > Department of Cell and Developmental Biology > Röntgenstrasse 20, 48149 Münster, Germany > Tel: +49-251-70365-324; Fax: +49-251-70365-399 > Email: vlad.cojocaru[at]mpi-muenster.mpg.de > > > _______________________________________________ > 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 Oct 25 2013 - 12:00:03 PDT