Make sure the directory you are running the calculation in is completely
free of mm_pbsa.pl output files before running the calculation, and then try
again.
If the error still exists, I would suggest you try using the python version
(MMPBSA.py) instead. MMPBSA.py just underwent a major overhaul in AmberTools
1.5 (which just got released!) that was designed to make it much more
user-friendly and much less error prone.
I hope that helps.
-Bill
On Sun, Apr 17, 2011 at 8:34 AM, mirage . <m.o.m.live.fr> wrote:
>
> Hi,Any Help??!!
>
> > From: m.o.m.live.fr
> > To: amber.ambermd.org
> > Date: Thu, 14 Apr 2011 07:30:46 +0000
> > Subject: [AMBER] No data for 0+0 MM BOND 0
> >
> >
> > Hi Amber users,
> >
> > My MM_PBSA calculation crash with (knowing that I have already done a
> lot of calculations with the same mmpbsa-input for similar complexes):
> >
> > =>> Values of parameters
> > TEMP = 300
> > R = 8.314
> > gammaP = 0.0072
> > betaP = 0.00
> > gammaG = 0.0072
> > betaG = 0.00
> > =>> Treat special parameters
> > =>> Calc missing parameters
> > Processing MM GAS
> > Doing 1 MM ELE
> > No values for MM_ELE existing -> Skipping
> > Processing MM INT
> > Doing 1 MM BOND
> > Doing 1 MM ANGLE
> > Doing 1 MM DIHED
> > Doing 1 MM BOND
> > Doing 1 MM ANGLE
> > Doing 1 MM DIHED
> > Doing 1 MM BOND
> > Doing 1 MM ANGLE
> > Doing 1 MM DIHED
> > Processing MM ELE
> > Doing 1 MM ELENB
> > Doing 1 MM ELE14
> > Doing 1 MM ELENB
> > Doing 1 MM ELE14
> > Doing 1 MM ELENB
> > Doing 1 MM ELE14
> > Processing MM VDW
> > Doing 1 MM VDWNB
> > Doing 1 MM VDW14
> > Doing 1 MM VDWNB
> > Doing 1 MM VDW14
> > Doing 1 MM VDWNB
> > Doing 1 MM VDW14
> > Processing GB GBTOT
> > Doing 1 GB GBSOL
> > No values for GB_GBSOL existing -> Skipping
> > Processing GB GBELE
> > Doing 1 GB GB
> > Doing 1 MM ELE
> > Doing 1 GB GB
> > Doing 1 MM ELE
> > Doing 1 GB GB
> > Doing 1 MM ELE
> > Processing GB GBSOL
> > Doing 1 GB GB
> > Doing 1 GB GBSUR
> > Doing 1 GB GB
> > Doing 1 GB GBSUR
> > Doing 1 GB GB
> > Doing 1 GB GBSUR
> > Processing PB PBSOL
> > Doing 1 PB PBCAL
> > Doing 1 PB PBSUR
> > Doing 1 PB PBDIS
> > Doing 1 PB PBCAL
> > Doing 1 PB PBSUR
> > Doing 1 PB PBDIS
> > Doing 1 PB PBCAL
> > Doing 1 PB PBSUR
> > Doing 1 PB PBDIS
> > Processing PB PBELE
> > Doing 1 PB PBCAL
> > Doing 1 MM ELE
> > Doing 1 PB PBCAL
> > Doing 1 MM ELE
> > Doing 1 PB PBCAL
> > Doing 1 MM ELE
> > Processing PB PBTOT
> > Doing 1 PB PBSOL
> > Doing 1 MM GAS
> > No values for MM_GAS existing -> Skipping
> > Processing MM GAS
> > Doing 1 MM ELE
> > Doing 1 MM VDW
> > Doing 1 MM INT
> > Doing 1 MM ELE
> > Doing 1 MM VDW
> > Doing 1 MM INT
> > Doing 1 MM ELE
> > Doing 1 MM VDW
> > Doing 1 MM INT
> > Processing GB GBTOT
> > Doing 1 GB GBSOL
> > Doing 1 MM GAS
> > Doing 1 GB GBSOL
> > Doing 1 MM GAS
> > Doing 1 GB GBSOL
> > Doing 1 MM GAS
> > Processing PB PBTOT
> > Doing 1 PB PBSOL
> > Doing 1 MM GAS
> > Doing 1 PB PBSOL
> > Doing 1 MM GAS
> > Doing 1 PB PBSOL
> > Doing 1 MM GAS
> > =>> Calc delta from raw data
> >
> >
> >
> >
> > /usr/spool/PBS/mom_priv/jobs/12908627.master0.alineos.net.SC: line 4:
> PBS: command not found
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1418.
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1418.
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1418.
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1391.
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1391.
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1391.
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1373.
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1373.
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1373.
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1442.
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1442.
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1442.
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1442.
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1442.
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1442.
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1442.
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1442.
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1442.
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1442.
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1442.
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1442.
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1537.
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1537.
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1537.
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1537.
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1537.
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1537.
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1537.
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1537.
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1537.
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1537.
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1537.
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1537.
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1537.
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1537.
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1537.
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1537.
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1537.
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1537.
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1537.
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1537.
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1537.
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1537.
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1537.
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1537.
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1537.
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1537.
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1537.
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1537.
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1537.
> > Use of uninitialized value in multiplication (*) at
> /home/AMBER-10/src/mm_pbsa/mm_pbsa_statistics.pm line 1537.
> > No data for 0+0 MM BOND 0
> >
> > Thanks in advance for annu help
> >
> >
> >
> >
> > _______________________________________________
> > 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
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Sun Apr 17 2011 - 06:30:03 PDT
