Hello again,
I solved the problem however I thing might be useful to refer here.
The problem was that _MMPBSA_receptor.mdcrd was badly created from
8 source 50 frames long trajectories (so 400 frames in total).
Interestingly only in case of the first analyzed trajectory
(prod46_PPI_A_mal.mdcrd)
the number of frames was correctly recognised:
Here is relevant record from the file _MMPBSA_ptraj3.out for this first
trajectory
----------------------------------------------------------------
PTRAJ: Processing input from file _MMPBSA_rectraj.in
PTRAJ: trajin ../mdcrdR/prod46_PPI_A_mal.mdcrd 1 400 1
Checking coordinates: ../mdcrdR/prod46_PPI_A_mal.mdcrd
Rank: 0 Atoms: 54011 FrameSize: 1312493 TitleSize: 81 NumBox: 3 Seekable 1
FYI ptrajSetupIO(): trajin stop value (400) is greater than the number of
sets read in.
Setting stop to the maximum value (50)
PTRAJ: strip :WAT:Cl-:CIO:Cs+:IB:K+:Li+:MG2:Na+:Rb+
Mask [:WAT:Cl-:CIO:Cs+:IB:K+:Li+:MG2:Na+:Rb+] represents 50517 atoms
---------------------------------------------------------------
In all remaining 7 cases ptraj from some strange reason was not able to
recognize the right number of the frames (50) and also to detect Wat ...
residues:
Here is for example relevant record from the file _MMPBSA_ptraj3.out for
prod47_PPI_A_mal.mdcrd
----------------------------------------------------------------------
PTRAJ: trajin ../mdcrdR/prod47_PPI_A_mal.mdcrd 1 400 1
Checking coordinates: ../mdcrdR/prod47_PPI_A_mal.mdcrd
checkCoordinates(): Could not predict number of frames for AMBER
trajectory file: ../mdcrdR/prod47_PPI_A_mal.mdcrd
If this is not a compressed file then there is a problem
Rank: 0 Atoms: 3494 FrameSize: 84970 TitleSize: 81 NumBox: 8 Seekable 0
PTRAJ: strip :WAT:Cl-:CIO:Cs+:IB:K+:Li+:MG2:Na+:Rb+
Mask [:WAT:Cl-:CIO:Cs+:IB:K+:Li+:MG2:Na+:Rb+] represents 0 atoms !!!NO
ATOMS DETECTED!!!
----------------------------------------------------------------------
The resulting trajectory _MMPBSA_receptor.mdcrd was then badly created as
the 50 + 7x400 frames (the most of them some "fake" frames).
The full records of the _MMPBSA_rectraj.in and _MMPBSA_ptraj3.out are
below.
I solved the problem by creating one trajectory from that 8 analysed in
separate
ptraj run (before the MMPBSA analysis).
When I provided this trajectory as the source mdcrd data, everything was
fine.
Best wishes,
Marek
#1 _MMPBSA_rectraj.in
trajin ../mdcrdR/prod46_PPI_A_mal.mdcrd 1 400 1
strip :WAT:Cl-:CIO:Cs+:IB:K+:Li+:MG2:Na+:Rb+
trajin ../mdcrdR/prod47_PPI_A_mal.mdcrd 1 400 1
strip :WAT:Cl-:CIO:Cs+:IB:K+:Li+:MG2:Na+:Rb+
trajin ../mdcrdR/prod48_PPI_A_mal.mdcrd 1 400 1
strip :WAT:Cl-:CIO:Cs+:IB:K+:Li+:MG2:Na+:Rb+
trajin ../mdcrdR/prod49_PPI_A_mal.mdcrd 1 400 1
strip :WAT:Cl-:CIO:Cs+:IB:K+:Li+:MG2:Na+:Rb+
trajin ../mdcrdR/prod50_PPI_A_mal.mdcrd 1 400 1
strip :WAT:Cl-:CIO:Cs+:IB:K+:Li+:MG2:Na+:Rb+
trajin ../mdcrdR/prod51_PPI_A_mal.mdcrd 1 400 1
strip :WAT:Cl-:CIO:Cs+:IB:K+:Li+:MG2:Na+:Rb+
trajin ../mdcrdR/prod52_PPI_A_mal.mdcrd 1 400 1
strip :WAT:Cl-:CIO:Cs+:IB:K+:Li+:MG2:Na+:Rb+
trajin ../mdcrdR/prod53_PPI_A_mal.mdcrd 1 400 1
strip :WAT:Cl-:CIO:Cs+:IB:K+:Li+:MG2:Na+:Rb+
trajout _MMPBSA_receptor.mdcrd nobox
--------------------------------------------------------
#2 _MMPBSA_ptraj3.out
\-/
-/- PTRAJ: a utility for processing trajectory files
/-\
\-/ Version: "AMBER 11.0 integrated" (4/2010)
-/- Executable is: "/home/mmaly/_applications/amber11_node25/bin/ptraj"
/-\ Running on 1 processor(s)
\-/ Residue labels:
CEN REP REP REP REP REP REP REP REP REP
REP REP REP REP REP REP REP REP REP REP
REP REP REP REP REP REP REP REP REP E10
E10 E10 E10 E10 E10 E10 E10 E10 E10 E10
...
E10 G4A G4A G4A G4A G4A G4A G4A G4A G4A
G4A G4A G4A G4A G4A G4A G4A G4A G4A G4A
...
G4A G4A G4A G4A G4A 0GA 0GA 0GA 0GA 0GA
0GA 0GA 0GA 0GA 0GA 0GA 0GA 0GA 0GA 0GA
...
0GA 0GA 0GA 0GA 0GA 0GA 0GA 0GA 0GA WAT
WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT
...
WAT WAT WAT WAT WAT WAT WAT WAT
PTRAJ: Processing input from file _MMPBSA_rectraj.in
PTRAJ: trajin ../mdcrdR/prod46_PPI_A_mal.mdcrd 1 400 1
Checking coordinates: ../mdcrdR/prod46_PPI_A_mal.mdcrd
Rank: 0 Atoms: 54011 FrameSize: 1312493 TitleSize: 81 NumBox: 3 Seekable 1
FYI ptrajSetupIO(): trajin stop value (400) is greater than the number of
sets read in.
Setting stop to the maximum value (50)
PTRAJ: strip :WAT:Cl-:CIO:Cs+:IB:K+:Li+:MG2:Na+:Rb+
Mask [:WAT:Cl-:CIO:Cs+:IB:K+:Li+:MG2:Na+:Rb+] represents 50517 atoms
PTRAJ: trajin ../mdcrdR/prod47_PPI_A_mal.mdcrd 1 400 1
Checking coordinates: ../mdcrdR/prod47_PPI_A_mal.mdcrd
checkCoordinates(): Could not predict number of frames for AMBER
trajectory file: ../mdcrdR/prod47_PPI_A_mal.mdcrd
If this is not a compressed file then there is a problem
Rank: 0 Atoms: 3494 FrameSize: 84970 TitleSize: 81 NumBox: 8 Seekable 0
PTRAJ: strip :WAT:Cl-:CIO:Cs+:IB:K+:Li+:MG2:Na+:Rb+
Mask [:WAT:Cl-:CIO:Cs+:IB:K+:Li+:MG2:Na+:Rb+] represents 0 atoms !!!NO
ATOMS DETECTED!!!
PTRAJ: trajin ../mdcrdR/prod48_PPI_A_mal.mdcrd 1 400 1
Checking coordinates: ../mdcrdR/prod48_PPI_A_mal.mdcrd
checkCoordinates(): Could not predict number of frames for AMBER
trajectory file: ../mdcrdR/prod48_PPI_A_mal.mdcrd
If this is not a compressed file then there is a problem
Rank: 0 Atoms: 3494 FrameSize: 84970 TitleSize: 81 NumBox: 8 Seekable 0
PTRAJ: strip :WAT:Cl-:CIO:Cs+:IB:K+:Li+:MG2:Na+:Rb+
Mask [:WAT:Cl-:CIO:Cs+:IB:K+:Li+:MG2:Na+:Rb+] represents 0 atoms !!!NO
ATOMS DETECTED!!!
PTRAJ: trajin ../mdcrdR/prod49_PPI_A_mal.mdcrd 1 400 1
Checking coordinates: ../mdcrdR/prod49_PPI_A_mal.mdcrd
checkCoordinates(): Could not predict number of frames for AMBER
trajectory file: ../mdcrdR/prod49_PPI_A_mal.mdcrd
If this is not a compressed file then there is a problem
Rank: 0 Atoms: 3494 FrameSize: 84970 TitleSize: 81 NumBox: 8 Seekable 0
PTRAJ: strip :WAT:Cl-:CIO:Cs+:IB:K+:Li+:MG2:Na+:Rb+
Mask [:WAT:Cl-:CIO:Cs+:IB:K+:Li+:MG2:Na+:Rb+] represents 0 atoms !!!NO
ATOMS DETECTED!!!
PTRAJ: trajin ../mdcrdR/prod50_PPI_A_mal.mdcrd 1 400 1
Checking coordinates: ../mdcrdR/prod50_PPI_A_mal.mdcrd
checkCoordinates(): Could not predict number of frames for AMBER
trajectory file: ../mdcrdR/prod50_PPI_A_mal.mdcrd
If this is not a compressed file then there is a problem
Rank: 0 Atoms: 3494 FrameSize: 84970 TitleSize: 81 NumBox: 8 Seekable 0
PTRAJ: strip :WAT:Cl-:CIO:Cs+:IB:K+:Li+:MG2:Na+:Rb+
Mask [:WAT:Cl-:CIO:Cs+:IB:K+:Li+:MG2:Na+:Rb+] represents 0 atoms !!!NO
ATOMS DETECTED!!!
PTRAJ: trajin ../mdcrdR/prod51_PPI_A_mal.mdcrd 1 400 1
Checking coordinates: ../mdcrdR/prod51_PPI_A_mal.mdcrd
checkCoordinates(): Could not predict number of frames for AMBER
trajectory file: ../mdcrdR/prod51_PPI_A_mal.mdcrd
If this is not a compressed file then there is a problem
Rank: 0 Atoms: 3494 FrameSize: 84970 TitleSize: 81 NumBox: 8 Seekable 0
PTRAJ: strip :WAT:Cl-:CIO:Cs+:IB:K+:Li+:MG2:Na+:Rb+
Mask [:WAT:Cl-:CIO:Cs+:IB:K+:Li+:MG2:Na+:Rb+] represents 0 atoms !!!NO
ATOMS DETECTED!!!
PTRAJ: trajin ../mdcrdR/prod52_PPI_A_mal.mdcrd 1 400 1
Checking coordinates: ../mdcrdR/prod52_PPI_A_mal.mdcrd
checkCoordinates(): Could not predict number of frames for AMBER
trajectory file: ../mdcrdR/prod52_PPI_A_mal.mdcrd
If this is not a compressed file then there is a problem
Rank: 0 Atoms: 3494 FrameSize: 84970 TitleSize: 81 NumBox: 8 Seekable 0
PTRAJ: strip :WAT:Cl-:CIO:Cs+:IB:K+:Li+:MG2:Na+:Rb+
Mask [:WAT:Cl-:CIO:Cs+:IB:K+:Li+:MG2:Na+:Rb+] represents 0 atoms !!!NO
ATOMS DETECTED!!!
PTRAJ: trajin ../mdcrdR/prod53_PPI_A_mal.mdcrd 1 400 1
Checking coordinates: ../mdcrdR/prod53_PPI_A_mal.mdcrd
checkCoordinates(): Could not predict number of frames for AMBER
trajectory file: ../mdcrdR/prod53_PPI_A_mal.mdcrd
If this is not a compressed file then there is a problem
Rank: 0 Atoms: 3494 FrameSize: 84970 TitleSize: 81 NumBox: 8 Seekable 0
PTRAJ: strip :WAT:Cl-:CIO:Cs+:IB:K+:Li+:MG2:Na+:Rb+
Mask [:WAT:Cl-:CIO:Cs+:IB:K+:Li+:MG2:Na+:Rb+] represents 0 atoms !!!NO
ATOMS DETECTED!!!
PTRAJ: trajout _MMPBSA_receptor.mdcrd nobox
../mdcrdR/prod46_PPI_A_mal.mdcrd: 50 frames.
../mdcrdR/prod47_PPI_A_mal.mdcrd: 772 frames.
../mdcrdR/prod48_PPI_A_mal.mdcrd: 772 frames.
../mdcrdR/prod49_PPI_A_mal.mdcrd: 772 frames.
../mdcrdR/prod50_PPI_A_mal.mdcrd: 772 frames.
../mdcrdR/prod51_PPI_A_mal.mdcrd: 772 frames.
../mdcrdR/prod52_PPI_A_mal.mdcrd: 772 frames.
../mdcrdR/prod53_PPI_A_mal.mdcrd: 772 frames.
PTRAJ: Successfully read the input file.
Coordinate processing will occur on 2850 frames.
Summary of I/O and actions follows:
INPUT COORDINATE FILES
File (../mdcrdR/prod46_PPI_A_mal.mdcrd) is an AMBER trajectory (with box
info) with 50 sets
File (../mdcrdR/prod47_PPI_A_mal.mdcrd) is an AMBER trajectory (with box
info) with 400 sets
File (../mdcrdR/prod48_PPI_A_mal.mdcrd) is an AMBER trajectory (with box
info) with 400 sets
File (../mdcrdR/prod49_PPI_A_mal.mdcrd) is an AMBER trajectory (with box
info) with 400 sets
File (../mdcrdR/prod50_PPI_A_mal.mdcrd) is an AMBER trajectory (with box
info) with 400 sets
File (../mdcrdR/prod51_PPI_A_mal.mdcrd) is an AMBER trajectory (with box
info) with 400 sets
File (../mdcrdR/prod52_PPI_A_mal.mdcrd) is an AMBER trajectory (with box
info) with 400 sets
File (../mdcrdR/prod53_PPI_A_mal.mdcrd) is an AMBER trajectory (with box
info) with 400 sets
OUTPUT COORDINATE FILE
File (_MMPBSA_receptor.mdcrd) is an AMBER trajectory
ACTIONS
1> STRIP: 50517 atoms will be removed from trajectory: :190-17028
2> STRIP: 0 atoms will be removed from trajectory: 3> STRIP: 0 atoms
will be removed from trajectory: 4> STRIP: 0 atoms will be removed from
trajectory: 5> STRIP: 0 atoms will be removed from trajectory: 6>
STRIP: 0 atoms will be removed from trajectory: 7> STRIP: 0 atoms will
be removed from trajectory: 8> STRIP: 0 atoms will be removed from
trajectory:
Processing AMBER trajectory file ../mdcrdR/prod46_PPI_A_mal.mdcrd
........................ 75% 100%
Processing AMBER trajectory file ../mdcrdR/prod47_PPI_A_mal.mdcrd
1% ............ 25% ............ 50% ............ 75% ............ 100%
Processing AMBER trajectory file ../mdcrdR/prod48_PPI_A_mal.mdcrd
1% ............ 25% ............ 50% ............ 75% ............ 100%
Processing AMBER trajectory file ../mdcrdR/prod49_PPI_A_mal.mdcrd
1% ............ 25% ............ 50% ............ 75% ............ 100%
Processing AMBER trajectory file ../mdcrdR/prod50_PPI_A_mal.mdcrd
1% ............ 25% ............ 50% ............ 75% ............ 100%
Processing AMBER trajectory file ../mdcrdR/prod51_PPI_A_mal.mdcrd
1% ............ 25% ............ 50% ............ 75% ............ 100%
Processing AMBER trajectory file ../mdcrdR/prod52_PPI_A_mal.mdcrd
1% ............ 25% ............ 50% ............ 75% ............ 100%
Processing AMBER trajectory file ../mdcrdR/prod53_PPI_A_mal.mdcrd
1% ............ 25% ............ 50% ............ 75% ............ 100%
PTRAJ: Successfully read in 2850 sets and processed 2850 sets.
Dumping accumulated results (if any)
Dne Fri, 18 Nov 2011 17:34:54 +0100 Marek Maly <marek.maly.ujep.cz>
napsal/-a:
> 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,
> /
>
>
--
Tato zpráva byla vytvořena převratným poštovním klientem Opery:
http://www.opera.com/mail/
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Received on Mon Nov 21 2011 - 03:30:02 PST
