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-- MM GB PB MS PB_SURFTEN 0.00542 PB_SURFOFF 0.92 GB_SURFTEN 0.0072 GB_SURFOFF 0.00 -- The GB in second line would me missing if GB was set to 0 in mm_pbsa.pl, but for some reason, it is required to be present in these files. Thanks! On Tue, Sep 14, 2010 at 11:06 PM, Jason Swails <jason.swails.gmail.com>wrote: > Does it work if you only do one snapshot? Don't forget to remove the files > that mm_pbsa.pl writes if you restart a simulation, since > mm_pbsa.pltypically appends to files, and you don't want it to append > to files that > begin with a failed calculation. This should help you pinpoint the problem > -- it could be that the prmtop files are incompatible with the > trajectories, > certain residues were improperly specified, etc. > > Hope this helps, > Jason > > On Tue, Sep 14, 2010 at 10:55 PM, manoj singh <mks.amber.gmail.com> wrote: > > > Thanks for the reply, > > > > Yes! I applied all bugfixes. This is Amber10. > > > > -- > > > > On Tue, Sep 14, 2010 at 10:52 PM, Jason Swails <jason.swails.gmail.com > > >wrote: > > > > > Have you applied all bugfixes? What version of amber are you using? > > > > > > On Tue, Sep 14, 2010 at 9:59 PM, manoj singh <mks.amber.gmail.com> > > wrote: > > > > > > > Hi, > > > > > > > > I am using mm_pbsa.pl to do per-residue decomposition. The > calculation > > > > appears to be trapped in a infinite loop with the following message. > I > > > have > > > > no clue what is going on and will be very thankful for any response. > > > > > > > > Manoj > > > > > > > > ----- > > > > > > > > No values for GB_TGBSUR existing -> Skipping > > > > Processing PB SPBSOL > > > > Doing 1 PB SPB > > > > Doing 1 GB SGBSUR > > > > No values for GB_SGBSUR existing -> Skipping > > > > Processing PB TPBTOT > > > > Doing 1 PB TPBSOL > > > > No values for PB_TPBSOL existing -> Skipping > > > > Processing PB BPBTOT > > > > Doing 1 PB BPBSOL > > > > No values for PB_BPBSOL existing -> Skipping > > > > Processing PB BPBSOL > > > > Doing 1 PB BPB > > > > Doing 1 GB BGBSUR > > > > No values for GB_BGBSUR existing -> Skipping > > > > Processing PB SPBTOT > > > > Doing 1 PB SPBSOL > > > > No values for PB_SPBSOL existing -> Skipping > > > > Processing PB TPBSOL > > > > Doing 1 PB TPB > > > > Doing 1 GB TGBSUR > > > > No values for GB_TGBSUR existing -> Skipping > > > > Processing PB SPBSOL > > > > Doing 1 PB SPB > > > > Doing 1 GB SGBSUR > > > > No values for GB_SGBSUR existing -> Skipping > > > > _______________________________________________ > > > > AMBER mailing list > > > > AMBER.ambermd.org > > > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > > > > > > > > > > > > -- > > > Jason M. Swails > > > Quantum Theory Project, > > > University of Florida > > > Ph.D. Graduate Student > > > 352-392-4032 > > > _______________________________________________ > > > 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 > > > > > > -- > Jason M. Swails > Quantum Theory Project, > University of Florida > Ph.D. Graduate Student > 352-392-4032 > _______________________________________________ > 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 Tue Sep 14 2010 - 20:30:04 PDT