Hello Bill,
The following was the error i got in MM_pbsa.pl ,why is it so happened
Use of uninitialized value in concatenation (.) or string at
/usr/local/packages/amber/11/intel-11.1-mvapich-1.1/src/mm_pbsa/
mm_pbsa_createinput.pm line 596.
Use of uninitialized value in concatenation (.) or string at
/usr/local/packages/amber/11/intel-11.1-mvapich-1.1/src/mm_pbsa/
mm_pbsa_createinput.pm line 596.
Use of uninitialized value in concatenation (.) or string at
/usr/local/packages/amber/11/intel-11.1-mvapich-1.1/src/mm_pbsa/
mm_pbsa_createinput.pm line 596.
Prmtop ./pdb1k4u_apo2.prmtop and coord.file ./snapshot_com.crd.1
have different atom numbers
For details see:
http://ambermd.org/Questions/mm_pbsa.html#check_atom_nr_prmtop_and_crd_differ
at
/usr/local/packages/amber/11/intel-11.1-mvapich-1.1/src/mm_pbsa/
mm_pbsa_calceneent.pm line 1137.
Thanks & Regards,
Vani
On Tue, Apr 5, 2011 at 3:56 PM, Bill Miller III <brmilleriii.gmail.com>wrote:
> The Bad magic number error has been mentioned by other users in previous
> threads, such as http://archive.ambermd.org/201103/0259.html. This means
> that the version of python being used to execute the python scripts is
> incompatible with the version of python that was used to originally compile
> the scripts. You will need to make sure you are using the same version of
> python to both compile and execute MMPBSA.py.
>
> Good luck!
>
> -Bill
>
> On Tue, Apr 5, 2011 at 4:44 PM, vani panguluri <vanipanguluri.gmail.com
> >wrote:
>
> > Hello,
> >
> > By using MMPBSA.py also i am getting the below error
> >
> > killing remote processes...Traceback (most recent call last):
> > File
> > "/usr/local/packages/amber/11/intel-11.1-mvapich-1.1/bin/MMPBSA.py.MPI",
> > line 43, in ?
> > import inputparse, utils, alamdcrd # (2)
> > ImportError: Bad magic number in
> > /home/packages/amber/11/intel-11.1-mvapich-1.1/bin/inputparse.pyc
> > MPI process terminated unexpectedly
> > 'import site' failed; use -v for traceback
> > Traceback (most recent call last):
> >
> > import sys, os, time, math # (1)
> > KeyboardInterrupt
> > 'import site' failed; use -v for traceback
> > 'import site' failed; use -v for traceback
> > 'import site' failed; use -v for traceback
> > 'import site' failed; use -v for traceback
> > 'import site' failed; use -v for traceback
> > File
> > "/usr/local/packages/amber/11/intel-11.1-mvapich-1.1/bin/MMPBSA.py.MPI",
> > line 43, in ?
> > import inputparse, utils, alamdcrd # (2)
> > ImportError: Bad magic number in
> > /home/packages/amber/11/intel-11.1-mvapich-1.1/bin/inputparse.pyc
> >
> > Could you please check that one.
> >
> > Regards,
> > Vani
> >
> > On Tue, Apr 5, 2011 at 1:29 PM, Jason Swails <jason.swails.gmail.com>
> > wrote:
> >
> > > mm_pbsa.pl has no MPI. If you are running Amber11, then it has an
> > option
> > > to
> > > fork processes (thereby running in parallel), but it is NOT MPI, and it
> > > can't be run on distributed systems (i.e., only one node). This is
> > > described in the manual.
> > >
> > > If you want to use an MPI version of MM/PBSA, you'll have to use the
> > Python
> > > version.
> > >
> > > All the best,
> > > Jason
> > >
> > > On Tue, Apr 5, 2011 at 11:06 AM, vani panguluri <
> vanipanguluri.gmail.com
> > > >wrote:
> > >
> > > > Hello Dwight,
> > > >
> > > > The following is the command
> > > > mpirun -np $NPROCS
> > > /usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/
> > > > mm_pbsa.pl binding_energy.mmpbsa > binding_energy.log
> > > >
> > > > and the binding_energy.mmpbsa is
> > > > .GENERAL
> > > > PREFIX snapshot
> > > > PATH ./
> > > > COMPLEX 1
> > > > RECEPTOR 1
> > > > LIGAND 1
> > > > COMPT ./pdb1k4u_apo2.prmtop
> > > > RECPT ./1k4u.prmtop
> > > > LIGPT ./apocynin.prmtop
> > > > GC 0
> > > > AS 0
> > > > DC 0
> > > > MM 1
> > > > GB 1
> > > > PB 1
> > > > MS 1
> > > > NM 0
> > > > .PB
> > > > PROC 2
> > > > REFE 0
> > > > INDI 1.0
> > > > EXDI 80.0
> > > > SCALE 2
> > > > LINIT 1000
> > > > PRBRAD 1.4
> > > > ISTRNG 0.0
> > > > RADIOPT 0
> > > > NPOPT 1
> > > > CAVITY_SURFTEN 0.0072
> > > > CAVITY_OFFSET 0.00
> > > > SURFTEN 0.0072
> > > > SURFOFF 0.00
> > > > .MM
> > > > DIELC 1.0
> > > > .GB
> > > > IGB 2
> > > > GBSA 1
> > > > SALTCON 0.00
> > > > EXTDIEL 80.0
> > > > INTDIEL 1.0
> > > > SURFTEN 0.0072
> > > > SURFOFF 0.00
> > > > .MS
> > > > PROBE 0.0
> > > >
> > > > could please check why i got that error.
> > > > Regards ,
> > > > Vani
> > > >
> > > > On Tue, Apr 5, 2011 at 10:37 AM, Dwight McGee <
> dwight.mcgee.gmail.com
> > > > >wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > Can you provide the following information so that it can help us
> > > > diagnose
> > > > > your problem. What did you specifically type on the command line to
> > run
> > > > > this
> > > > > calculation (inputs/outputs if any)? Have you applied all bug
> fixes?
> > Do
> > > > you
> > > > > pass all the amber tests when you run *test_amber_parallel.sh?*
> > > > >
> > > > > On Mon, Apr 4, 2011 at 7:11 PM, vani panguluri <
> > > vanipanguluri.gmail.com
> > > > > >wrote:
> > > > >
> > > > > > Hello amber users,
> > > > > >
> > > > > > I am get the following error while executing mm_pbsa.pl.
> > > > > >
> > > > > > Exit code -5 signaled from qb504
> > > > > > Killing remote processes... At-entry must be first
> > > > > > For details see:
> > > > > >
> > http://ambermd.org/Questions/mm_pbsa.html#read_input_at_entry_first
> > > > > > At-entry must be first For details see:
> > > > > >
> > http://ambermd.org/Questions/mm_pbsa.html#read_input_at_entry_first
> > > > > > At-entry must be first For details see:
> > > > > >
> > http://ambermd.org/Questions/mm_pbsa.html#read_input_at_entry_first
> > > > > > At-entry must be first For details see:
> > > > > >
> > http://ambermd.org/Questions/mm_pbsa.html#read_input_at_entry_first
> > > > > > MPI process terminated unexpectedly
> > > > > > DONE
> > > > > > ------------------------------------------------------
> > > > > > Running PBS epilogue script - 04-Apr-2011 18:06:06
> > > > > > ------------------------------------------------------
> > > > > > Checking node qb504 (MS)
> > > > > > -> Killing process of vani: bash
> > > > > > -> Killing process of vani:
> > > > > > /home/packages/mvapich/1.1/intel-11.1/bin/mpispawn
> > > > > > -> Killing process of vani: [mm_pbsa.pl]
> > > > > > /usr/local/sbin/node_cleaner: line 86: kill: (3307) - No such
> > process
> > > > > > -> Killing process of vani: [mm_pbsa.pl]
> > > > > > /usr/local/sbin/node_cleaner: line 86: kill: (3308) - No such
> > > process->
> > > > > > Killing process of vani: [mm_pbsa.pl]
> > > > > > /usr/local/sbin/node_cleaner: line 86: kill: (3309) - No such
> > process
> > > > > > -> Killing process of vani: [mm_pbsa.pl
> > > ]/usr/local/sbin/node_cleaner:
> > > > > line
> > > > > > 86: kill: (3310) - No such process
> > > > > > -> Killing process of vani: [mm_pbsa.pl]
> > > > > > /usr/local/sbin/node_cleaner: line 86: kill: (3311) - No such
> > > process->
> > > > > > Killing process of vani: [mm_pbsa.pl]
> > > > > > /usr/local/sbin/node_cleaner: line 86: kill: (3313) - No such
> > process
> > > > > > -> Killing process of vani: [mm_pbsa.pl
> > > ]/usr/local/sbin/node_cleaner:
> > > > > line
> > > > > > 86: kill: (3314) - No such process
> > > > > > Checking node qb504 ok
> > > > > >
> > > > > >
> > > > > > can anyone help me to solve this error.
> > > > > >
> > > > > > Regards,
> > > > > > Vani
> > > > > > _______________________________________________
> > > > > > AMBER mailing list
> > > > > > AMBER.ambermd.org
> > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > >
> > > > >
> > > > >
> > > > >
> > > > > --
> > > > > T. Dwight McGee Jr.
> > > > > Quantum Theory Project
> > > > > University of Florida
> > > > > Graduate Student
> > > > > dwight.mcgee.gmail.com
> > > > >
> > > > > "Problems cannot be solved at the same level of awareness that
> > created
> > > > > them."
> > > > > Albert Einstein
> > > > > _______________________________________________
> > > > > 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. Candidate
> > > 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
> >
>
>
>
> --
> Bill Miller III
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-6715
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Apr 05 2011 - 15:30:03 PDT
