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
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Received on Thu Apr 02 2015 - 06:30:07 PDT
