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
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Received on Sun Jan 06 2013 - 16:00:03 PST
