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-- Ray Luo, Ph.D. Professor, Biochemistry, Molecular Biophysics, and Biomedical Engineering University of California, Irvine, CA 92697-3900 On Fri, Dec 20, 2013 at 9:14 AM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote: > Vlad, > > Thanks a lot for sharing your data! Wes will run your job both ways to > see how thing goes … > > Ray > -- > Ray Luo, Ph.D. > Professor, > Biochemistry, Molecular Biophysics, and > Biomedical Engineering > University of California, Irvine, CA 92697-3900 > > > On Fri, Dec 20, 2013 at 6:12 AM, Vlad Cojocaru > <vlad.cojocaru.mpi-muenster.mpg.de> wrote: > > Hi Ray, > > > > Please find attached an archive with a test directory as I promised. > > Please note in the attached files the input parameter "sasopt" is set to > 0 > > ... With this setting, the MMPBSA ran successfully ... In order to > reproduce > > my error you need to set this parameter to 1, which in the case of inp=1 > is > > required anyhow. > > > > Thanks a lot for looking into this ... > > > > Best wishes > > Vlad > > > > P.S. The files belong to an unpublished project (soon to be submitted), > so > > please keep everything confidential. Thanks > > > > > > > > > > On 12/19/2013 07:44 PM, Vlad Cojocaru wrote: > >> > >> HI Ray, > >> > >> Off list ... Yes, I can send you some snapshots but only tomorrow as > now I > >> am not in the office anymore ... > >> > >> Best, > >> Vlad > >> > >> > >> > >> On 12/19/2013 07:34 PM, Ray Luo, Ph.D. wrote: > >>> > >>> Vlad, > >>> > >>> Okat, input file looks fine to me. Can you email me off the list a few > >>> snapshots for us to reproduce your error? > >>> > >>> Ray > >>> On Dec 19, 2013 10:30 AM, "Vlad Cojocaru" > >>> <vlad.cojocaru.mpi-muenster.mpg.de> > >>> wrote: > >>> > >>>> Hi Ray, > >>>> > >>>> Below is the input and the running command (using the _MMPBSA_pb.mdin > >>>> file from my previous email)... > >>>> > >>>> Best wishes > >>>> Vlad > >>>> > >>>> > >>>> > >>>> cat << EOF > mmpbsa.in > >>>> MMPBSA > >>>> &general > >>>> debug_printlevel=0, > >>>> startframe=1, > >>>> endframe=50000, > >>>> interval=1, > >>>> keep_files=1, > >>>> netcdf=1, > >>>> ligand_mask=":1-152", > >>>> receptor_mask=":153-283", > >>>> use_sander=1, > >>>> entropy=0, > >>>> full_traj=1, > >>>> verbose=2, > >>>> / > >>>> &pb > >>>> inp=1, > >>>> cavity_offset=0.86, > >>>> cavity_surften=0.005, > >>>> indi=1.0, > >>>> exdi=80.0, > >>>> fillratio=4.0, > >>>> istrng=0.100, > >>>> linit=1000, > >>>> prbrad=1.4, > >>>> radiopt=0, > >>>> scale=2.0, > >>>> / > >>>> EOF > >>>> > >>>> $AMBERHOME/bin/MMPBSA.py.MPI -O -i mmpbsa.in \ > >>>> -o mmpbsa.out \ > >>>> -cp complex.top \ > >>>> -rp receptor.top \ > >>>> -lp ligand.top \ > >>>> -y complex.cdf \ > >>>> -eo energy.out \ > >>>> -use-mdins > >>>> > >>>> > >>>> > >>>> > >>>> On 12/19/2013 06:40 PM, Ray Luo, Ph.D. wrote: > >>>>> > >>>>> Vlad, > >>>>> > >>>>> Please show us your "mmpbsa.in" file. > >>>>> > >>>>> Ray > >>>>> On Dec 19, 2013 2:40 AM, "Vlad Cojocaru" < > >>>> > >>>> vlad.cojocaru.mpi-muenster.mpg.de> > >>>>> > >>>>> wrote: > >>>>> > >>>>>> Dear all, > >>>>>> > >>>>>> I am trying an MMPBSA calculation (AmberTools 13) with inp=1 (see > >>>>>> input > >>>>>> file below). However I get a PB Bomb error (see below). > >>>>>> Now, reading through the list archive, it was reported a while ago > >>>>>> (2011) that this might have something to do with sasopt=1 in the > input > >>>>>> file. Howeever, this is required for inp=1 ... That thread had no > >>>>>> answers though. Does anybody have any experience with this type of > >>>>>> errors ? Anything obviously wrong in my input ?. I created the input > >>>>>> upon systematically reading the original literature on the > parameters > >>>>>> . > >>>>>> > >>>>>> Thanks for any advice on this, > >>>>>> > >>>>>> Best wishes > >>>>>> Vlad > >>>>>> > >>>>>> > >>>>>> ****************** Sander input for PB calculation > >>>>>> ********************* > >>>>>> File generated by MMPBSA.py > >>>>>> &cntrl > >>>>>> nsnb=99999, dec_verbose=0, ioutfm=1, > >>>>>> ipb=2, ntb=0, cut=999.0, imin=5, > >>>>>> igb=10, inp=1, > >>>>>> / > >>>>>> &pb > >>>>>> epsin=1, epsout=80, smoothopt=1, > >>>>>> istrng=100.0, pbtemp=300, radiopt=0, > >>>>>> dprob=1.4, iprob=2.0, sasopt=1, saopt=0, > >>>>>> triopt=1, arcres=0.25, > >>>>>> npbopt=0, solvopt=1, accept=0.001, > >>>>>> maxitn=100, fillratio=4.0, space=0.5, > >>>>>> nbuffer=0, nfocus=2, fscale=8, npbgrid=1, > >>>>>> bcopt=5, eneopt=2, frcopt=0, scalec=0, > >>>>>> cutfd=5.0, cutnb=0, nsnba=1, > >>>>>> phiout=0, > >>>>>> decompopt=2, use_rmin=1, sprob=1.4, vprob=1.4, > >>>>>> rhow_effect=1.0, use_sav=0, > >>>>>> cavity_surften=0.005, cavity_offset=0.86, > >>>>>> maxsph=400, > >>>>>> / > >>>>>> > >>>>>> ****************** Error ***************************** > >>>>>> PB Bomb in assignlvlset(): no atmsas 105 97 7 > >>>>>> 103 95 9 -2 > >>>>>> 103 95 9 -2 > >>>>>> 103 95 9 -2 > >>>>>> 103 95 9 -2 > >>>>>> 103 95 9 -2 > >>>>>> 103 95 9 2 > >>>>>> 103 95 9 -2 > >>>>>> PB Bomb in assignlvlset(): illegal insas flag 105 97 7 -4 > >>>>>> > >>>>>> -- > >>>>>> 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 > > http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru > > > _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Mon Dec 23 2013 - 12:00:02 PST