also full log of the error
Loading and checking parameter files for compatibility...
sander found! Using /home/cmoon/Prog/amber12/bin/sander
cpptraj found! Using /home/cmoon/Prog/amber12/bin/cpptraj
Preparing trajectories for simulation...
120 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning GB calculations with /home/cmoon/Prog/amber12/bin/sander
calculating complex contribution...
CalcError: /home/cmoon/Prog/amber12/bin/sander failed with prmtop
/home/cmoon/argh/OR5P3_allyl-phenyl-acetate/decomposition_OR5P3_allyl-phenyl-acetate/complex.prmtop!
Error occured on rank 2.
Exiting. All files have been retained.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2
CalcError: /home/cmoon/Prog/amber12/bin/sander failed with prmtop
/home/cmoon/argh/OR5P3_allyl-phenyl-acetate/decomposition_OR5P3_allyl-phenyl-acetate/complex.prmtop!
Error occured on rank 1.
Exiting. All files have been retained.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1
CalcError: /home/cmoon/Prog/amber12/bin/sander failed with prmtop
/home/cmoon/argh/OR5P3_allyl-phenyl-acetate/decomposition_OR5P3_allyl-phenyl-acetate/complex.prmtop!
Error occured on rank 5.
Exiting. All files have been retained.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 5
CalcError: /home/cmoon/Prog/amber12/bin/sander failed with prmtop
/home/cmoon/argh/OR5P3_allyl-phenyl-acetate/decomposition_OR5P3_allyl-phenyl-acetate/complex.prmtop!
Error occured on rank 7.
Exiting. All files have been retained.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 7
[proxy:0:0.iREMB-S-16] HYDT_dmxu_poll_wait_for_event
(./tools/demux/demux_poll.c:70): assert (!(pollfds[i].revents &
~POLLIN & ~POLLOUT & ~POLLHUP)) failed
[proxy:0:0.iREMB-S-16] main (./pm/pmiserv/pmip.c:387): demux engine
error waiting for event
[mpiexec.iREMB-S-16] HYDT_bscu_wait_for_completion
(./tools/bootstrap/utils/bscu_wait.c:101): one of the processes
terminated badly; aborting
[mpiexec.iREMB-S-16] HYDT_bsci_wait_for_completion
(./tools/bootstrap/src/bsci_wait.c:18): bootstrap device returned
error waiting for completion
[mpiexec.iREMB-S-16] HYD_pmci_wait_for_completion
(./pm/pmiserv/pmiserv_pmci.c:521): bootstrap server returned error
waiting for completion
[mpiexec.iREMB-S-16] main (./ui/mpich/mpiexec.c:548): process manager
error waiting for completion
~
2015-04-02 17:08 GMT+02:00 James Starlight <jmsstarlight.gmail.com>:
> what I found on the bottom
>
>
> FATAL: NATOM mismatch in coord and topology files
>
>
> I've checked all topologies and it seems ok for me
>
> n atoms of complex.prmtop = n atoms of receptor.prmtop + n atoms of
> ligand.prmtop
>
> it;s strange because I don't see here where the coordinate file (smth
> like protein.inpcrd) are provided in the below mmgbsa input
>
> mpirun -np 16 MMPBSA.py.MPI -O -i mmgbsa.in -o
> mmgbsa_nm_OR5P3_quinoline.dat -sp
> /home/cmoon/argh/OR5P3_quinoline/protein.parm7 -cp
> /home/cmoon/argh/OR5P3_quinoline/decomposition_OR5P3_quinoline/complex.prmtop
> -rp /home/cmoon/argh/OR5P3_quinoline/decomposition_OR5P3_quinoline/receptor.prmtop
> -y /home/cmoon/argh/OR5P3_quinoline/md3.nc -lp
> /home/cmoon/argh/OR5P3_quinoline/decomposition_OR5P3_quinoline/ligand.prmtop
>> progress.log 2>&1
>
>
>
> 2015-04-02 16:50 GMT+02:00 Kenneth Huang <kennethneltharion.gmail.com>:
>> James,
>>
>> Generally speaking, you can always make the stripped topologies you need in
>> tleap, usually before you add ions and solvent, or you could just reload
>> your starting structure into tleap and save it without solvent/ions. That
>> said, ante-MMPBSA is good for when you don't have your starting structure
>> anymore, or don't want to backtrack, or don't know what masks you want to
>> use.
>>
>> As for your error, try checking the MMPBSA gb mdout file- it should give
>> you a more descriptive error message.
>>
>> Best,
>>
>> Kenneth
>>
>> On Thursday, April 2, 2015, James Starlight <jmsstarlight.gmail.com
>> <javascript:_e(%7B%7D,'cvml','jmsstarlight.gmail.com');>> wrote:
>>
>>> Dear Friends!
>>>
>>> I've faced with the problem during mmgbsa analysis of my system:
>>>
>>>
>>>
>>> Firstly I have no problems with processing of initial protein.parm7
>>> obtained using
>>>
>>> ante-MMPBSA.py -p ${sim}/protein.parm7 -c
>>> ${sim}/decomposition_${simulation}/complex.prmtop -r
>>> ${sim}/decomposition_${simulation}/receptor.prmtop -l
>>> ${sim}/decomposition_${simulation}/ligand.prmtop -s
>>> :WAT:Cl-:NA+:K+:PPC -n :MOL
>>>
>>> Stripping :WAT:Cl-:NA+:K+:PPC (solvent) from original topology, output
>>> is
>>> /home/cmoon/total_decomp/OR5P3_androstenone/decomposition_OR5P3_androstenone/complex.prmtop
>>> Done stripping solvent!
>>>
>>> Creating receptor topology file by stripping :MOL from
>>>
>>> /home/cmoon/total_decomp/OR5P3_androstenone/decomposition_OR5P3_androstenone/complex.prmtop
>>> Done creating receptor topology file!
>>>
>>> Creating ligand topology file by stripping !(:MOL) from
>>>
>>> /home/cmoon/total_decomp/OR5P3_androstenone/decomposition_OR5P3_androstenone/complex.prmtop
>>> Done creating ligand topology file!
>>>
>>>
>>>
>>> but then during decomposition using mmgbsa.py I've obtained error at
>>> the begining of calculations:
>>> (here the input file consisted of paths because it was produced by my
>>> bash script)
>>> mpirun -np 16 MMPBSA.py.MPI -O -i mmgbsa.in -o
>>> mmgbsa_nm_OR5P3_androstenone.dat -sp
>>> /home/cmoon/total_decomp/OR5P3_androstenone/protein.parm7 -cp
>>> complex.prmtop -rp receptor.prmtop -y
>>> /home/cmoon/total_decomp/OR5P3_androstenone/md1.nc
>>> /home/cmoon/total_decomp/OR5P3_androstenone/md2.nc
>>> /home/cmoon/total_decomp/OR5P3_androstenone/md3.nc -lp ligand.prmtop >
>>> progress.log 2>&1
>>>
>>> ::
>>> Running calculations on normal system...
>>>
>>> Beginning GB calculations with /home/cmoon/Prog/amber12/bin/sander
>>> calculating complex contribution...
>>> CalcError: /home/cmoon/Prog/amber12/bin/sander failed with prmtop
>>> complex.prmtop!
>>> Error occured on rank 3.
>>> Exiting. All files have been retained.
>>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 3
>>> APPLICATION TERMINATED WITH THE EXIT STRING: Hangup (signal 1)
>>>
>>> I've checked all prmtop files used here but have not found any errors
>>> here (the atom numbers and its composition is correct in all 3
>>> topologies made by ante-mmbsa). Could someone suggest me some
>>> resolution if the issue and alternative method to made stripped
>>> topologies avoiding ante-mmbsa?
>>>
>>> Thanks!!
>>>
>>> James
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>> --
>> Ask yourselves, all of you, what power would hell have if those imprisoned
>> here could not dream of heaven?
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Thu Apr 02 2015 - 08:30:05 PDT
