Hello all,
I am just wondering if MMPBSA.py natively supports 2 trajectory approach
in MMPBSA/GBSA analysis.
It means:
COMPLEX and LIGAND take from the COMPLEX trajectories and RECEPTOR from
the separate RECEPTOR trajectory.
In my case it failed with this error significant for both GB/PB however
written in different calc. stages:
---------------------------------------------
IOError: [Errno 9] Bad file descriptor
close failed in file object destructor:
---------------------------------------------
Lets just note, that in case of 1-trajectory analysis everything was OK,
and GB/PB analyses were done in few minutes.
I used this command to run the 2-traj approach analysis:
.
.
.
SOLV_COM_PRMTOP="../prmtop/com_solvated.prmtop"
SOLV_REC_PRMTOP="../prmtop/rec_solvated.prmtop"
COM_PRMTOP="../prmtop/com.prmtop"
REC_PRMTOP="../prmtop/rec.prmtop"
LIG_PRMTOP="../prmtop/lig.prmtop"
#Complex trajectories
MDCRD="../mdcrd/*.*"
#Receptortrajectories
MDCRDR="../mdcrdR/*.*"
mpiexec -ppn $PPN -n $CPUS $EXE -O -i $IN -o $OUT -sp $SOLV_COM_PRMTOP
-srp $SOLV_REC_PRMTOP -cp $COM_PRMTOP -rp $REC_PRMTOP -lp $LIG_PRMTOP -y
$MDCRD -yr $MDCRDR > progress.log 2>&1
.
.
.
and obtained below written errors.
Thanks a lot in adavnce for any relevant comments !
Best wishes,
Marek
GB analysis
-----------------------------------------------------------------------------------
.
.
.
Beginning GB calculations with mmpbsa_py_energy...
calculating complex contribution...
calculating receptor contribution...
close failed in file object destructor:
IOError: [Errno 9] Bad file descriptor
close failed in file object destructor:
IOError: [Errno 9] Bad file descriptor
close failed in file object destructor:
IOError: [Errno 9] Bad file descriptor
close failed in file object destructor:
IOError: [Errno 9] Bad file descriptor
close failed in file object destructor:
IOError: [Errno 9] Bad file descriptor
close failed in file object destructor:
IOError: [Errno 9] Bad file descriptor
close failed in file object destructor:
IOError: [Errno 9] Bad file descriptor
calculating ligand contribution....
.
.
----------------------------------------------------------------------------------------
and these fro PB analysis:
-------------------------------------------------------------------------------------------
Beginning PB calculations with mmpbsa_py_energy...
calculating complex contribution...
PB Info in pb_read(): npopt has been overwritten with inp
PB Info in pb_read(): npopt has been overwritten with inp
PB Info in pb_read(): npopt has been overwritten with inp
PB Info in pb_read(): npopt has been overwritten with inp
PB Info in pb_read(): npopt has been overwritten with inp
PB Info in pb_read(): npopt has been overwritten with inp
PB Info in pb_read(): npopt has been overwritten with inp
PB Info in pb_read(): npopt has been overwritten with inp
Total surface charge 4.9329
Reaction field energy -2310.3467
Total surface charge 4.9825
Reaction field energy -2342.6606
Cavity solvation energy 58.6062
.
.
.
calculating receptor contribution...
PB Info in pb_read(): npopt has been overwritten with inp
Total surface charge 0.0380
Reaction field energy -2144.5485
Cavity solvation energy 61.0186
Total surface charge -0.0008
Reaction field energy -2199.3998
Cavity solvation energy 62.8272
.
.
.
calculating ligand contribution...
PB Info in pb_read(): npopt has been overwritten with inp
Total surface charge 4.9370
Reaction field energy -470.0802
Cavity solvation energy 12.3647
Total surface charge 4.9370
Reaction field energy -470.7943
Cavity solvation energy 12.1741
Total surface charge 4.9367
.
.
.
Total surface charge 4.9364
Reaction field energy -494.3758
Cavity solvation energy 11.5280
close failed in file object destructor:
IOError: [Errno 9] Bad file descriptor
----------------------------------------------------------------
INPUT FILES
GB
Input file for running PB and GB
&general
endframe=400, verbose=2, keep_files=2,
/
&gb
igb=1, saltcon=0.0
/
------------------------------------------
PB
Input file for running PB and GB
&general
endframe=400, verbose=2, keep_files=2,
/
&pb
istrng=0.0,
/
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Received on Fri Nov 18 2011 - 09:00:04 PST
