Hi Jason,
Thanks a lot for your answer.
I tried to use other machine that has a correct installation although i have a very limited quota on it just to see how the QM/MM binding energy goes on.
I want to use the dispersion corrected AM1 "AM1-D*" option via the -make-mdins and the -use-mdins- regime..I'm noticing that once the new job starts it deletes the input files and give an error unless i quickly recopy the inputs again to the working directory, i tried the "keep_files=2" command but it didn't work..Could you please advice..
Thanks a lot
Marawan
________________________________
From: Jason Swails <jason.swails.gmail.com>
To: marawan hussain <marawanhussain.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Monday, 7 January 2013 11:11 AM
Subject: Re: [AMBER] MMPBSA error
My mistake. It would have a .1 appended, not a .0, if my original
explanation was correct. Since your file names do have a .1 appended, I
suspect that's what happened.
After you update your serial installation, MMPBSA.py should work fine.
HTH,
Jason
On Sun, Jan 6, 2013 at 6:28 PM, marawan hussain <marawanhussain.yahoo.com>wrote:
> HI Jason,
> i have checked the produced files but the dummycomplex seems to already
> exist without the "0" appended to it.
> Here are the list of the produced files:
>
>
> com_solvated_t9.top
> com_t9.top
> _MMPBSA_complex_gb.mdout.0
> _MMPBSA_complex_gb.mdout.1
> _MMPBSA_complex_gb.mdout.2
> _MMPBSA_complex_gb.mdout.3
> _MMPBSA_complex_gb.mdout.4
> _MMPBSA_complex_gb.mdout.5
> _MMPBSA_complex_gb.mdout.6
> _MMPBSA_complex_gb.mdout.7
> _MMPBSA_complex.mdcrd.0
> _MMPBSA_complex.mdcrd.1
> _MMPBSA_complex.mdcrd.2
> _MMPBSA_complex.mdcrd.3
> _MMPBSA_complex.mdcrd.4
> _MMPBSA_complex.mdcrd.5
> _MMPBSA_complex.mdcrd.6
> _MMPBSA_complex.mdcrd.7
> _MMPBSA_complex.pdb
> _MMPBSA_dummycomplex.inpcrd.1
> _MMPBSA_dummyligand.inpcrd.1
> _MMPBSA_dummyreceptor.inpcrd.1
> _MMPBSA_gb.mdin
> _MMPBSA_gb_qmmm_com.mdin
> _MMPBSA_gb_qmmm_lig.mdin
> _MMPBSA_gb_qmmm_rec.mdin
> _MMPBSA_ligand.mdcrd.0
> _MMPBSA_ligand.mdcrd.1
> _MMPBSA_ligand.mdcrd.2
> _MMPBSA_ligand.mdcrd.3
> _MMPBSA_ligand.mdcrd.4
> _MMPBSA_ligand.mdcrd.5
> _MMPBSA_ligand.mdcrd.6
> _MMPBSA_ligand.mdcrd.7
> _MMPBSA_ligand.pdb
> _MMPBSA_normal_traj_cpptraj.out
> mmpbsa_py_energy
> _MMPBSA_receptor.mdcrd.0
> _MMPBSA_receptor.mdcrd.1
> _MMPBSA_receptor.mdcrd.2
> _MMPBSA_receptor.mdcrd.3
> _MMPBSA_receptor.mdcrd.4
> _MMPBSA_receptor.mdcrd.5
> _MMPBSA_receptor.mdcrd.6
> _MMPBSA_receptor.mdcrd.7
> _MMPBSA_receptor.pdb
> pbsa
> pbsa.e320054
> pbsa.in
> pbsa.o320054
> prod_nvt_2_her2.mdcrd
> rec_t9.top
> t9.top
>
>
> Below is the error file. please advice. Do you think that the problem may
> be related for different installations directories between the serial and
> parallel version.
>
> Thanks in advance.
> Marawan
>
>
> Error opening unit 30: File "_MMPBSA_dummycomplex.inpcrd" is missing or
> unreadable
>
> Error opening unit 30: File "_MMPBSA_dummycomplex.inpcrd" is missing
> or unreadable
>
> Error opening unit 30: File "_MMPBSA_dummycomplex.inpcrd" is missing
> or unreadable
> CalcError: /usr/local/amber12/bin/sander failed with prmtop com_t9.top!
> Error occured on rank 1.
> Exiting. All files have been retained.
> CalcError: /usr/local/amber12/bin/sander failed with prmtop com_t9.top!
> Error occured on rank 4.
> Exiting. All files have been retained.
> CalcError: /usr/local/amber12/bin/sander failed with prmtop com_t9.top!
> Error occured on rank 6.
> Exiting. All files have been retained.
>
> Error opening unit 30: File "_MMPBSA_dummycomplex.inpcrd" is missing
> or unreadable
>
> Error opening unit 30: File "_MMPBSA_dummycomplex.inpcrd" is missing
> or unreadable
> CalcError: /usr/local/amber12/bin/sander failed with prmtop com_t9.top!
> Error occured on rank 2.
> Exiting. All files have been retained.
> CalcError: /usr/local/amber12/bin/sander failed with prmtop com_t9.top!
> Error occured on rank 3.
> Exiting. All files have been retained.
>
> Error opening unit 30: File "_MMPBSA_dummycomplex.inpcrd" is missing
> or unreadable
> CalcError: /usr/local/amber12/bin/sander failed with prmtop com_t9.top!
> Error occured on rank 0.
> Exiting. All files have been retained.
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 6 in communicator MPI_COMM_WORLD
> with errorcode 1.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> --------------------------------------------------------------------------
>
> Error opening unit 30: File "_MMPBSA_dummycomplex.inpcrd" is missing
> or unreadable
> CalcError: /usr/local/amber12/bin/sander failed with prmtop com_t9.top!
> Error occured on rank 5.
> Exiting. All files have been retained.
>
> Error opening unit 30: File "_MMPBSA_dummycomplex.inpcrd" is missing
> or unreadable
> CalcError: /usr/local/amber12/bin/sander failed with prmtop com_t9.top!
> Error occured on rank 7.
> Exiting. All files have been retained.
> --------------------------------------------------------------------------
> mpirun has exited due to process rank 6 with PID 14806 on
> node sstar105.hpc.swin.edu.au exiting improperly. There are two reasons
> this could occur:
>
> 1. this process did not call "init" before exiting, but others in
> the job did. This can cause a job to hang indefinitely while it waits
> for all processes to call "init". By rule, if one process calls "init",
> then ALL processes must call "init" prior to termination.
>
> 2. this process called "init", but exited without calling "finalize".
> By rule, all processes that call "init" MUST call "finalize" prior to
> exiting or it will be considered an "abnormal termination"
>
> This may have caused other processes in the application to be
> terminated by signals sent by mpirun (as reported here).
> --------------------------------------------------------------------------
> [sstar105.hpc.swin.edu.au:14799] 7 more processes have sent help message
> help-mpi-api.txt / mpi-abort
> [sstar105.hpc.swin.edu.au:14799] Set MCA parameter
> "orte_base_help_aggregate" to 0 to see all help / error messages
>
>
>
>
>
>
>
>
>
>
> ________________________________
> From: Jason Swails <jason.swails.gmail.com>
> To: marawan hussain <marawanhussain.yahoo.com>; AMBER Mailing List <
> amber.ambermd.org>
> Sent: Saturday, 5 January 2013 3:19 AM
> Subject: Re: [AMBER] MMPBSA error
>
>
>
>
>
> On Thu, Jan 3, 2013 at 9:04 PM, marawan hussain <marawanhussain.yahoo.com>
> wrote:
>
> HI Jason,
> >Thanks a lot, now it works, but it gives me the following error:
> >
> > Error opening unit 30: File "_MMPBSA_dummycomplex.inpcrd" is missing
> or unreadable
> >
> > Error opening unit 30: File "_MMPBSA_dummycomplex.inpcrd" is missing
> or unreadable
> >
> > Error opening unit 30: File "_MMPBSA_dummycomplex.inpcrd" is missing
> or unreadable
> >CalcError: /usr/local/amber12/bin/sander failed with prmtop com_t9.top!
> >Error occured on rank 3.
> >
>
> Does the _MMPBSA_dummycomplex.inpcrd file exist? If not, is it named
> _MMPBSA_dummycomplex.inpcrd.0? If it has a '0' appended to it, then the
> likely explanation is that the cpptraj you are using is outdated.
> Specifically, bugfix.9 will correctly name this file (without the .0). If
> the file exists, but has .0 appended to it, then please update your cpptraj
> program and try again. (I presume that your parallel installation has
> bugfix.9 installed but your serial version does not)
>
> Also, this will only affect MMPBSA.py when sander is being used for the
> calculations (since mmpbsa_py_energy does not require an inpcrd file),
> which would explain why the calculation works when you take away the QM/MM
> part.
>
> HTH,
> Jason
> --
> 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
>
--
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
Received on Mon Jan 07 2013 - 03:00:04 PST
