The `/share/apps/amber11/bin/MMPBSA` file is a shell script which cannot
be interpreted by Python (therefore the error). Remove the
`/share/apps/amber11/bin/python2.6` from your command.
Jan-Philip
On 08/22/2011 06:12 PM, Osman, Roman wrote:
> Seungyeul,
> I used the following path:
> MMPBSA=/share/apps/amber11/bin/MMPBSA
> and it gave me an error:
> /share/apps/amber11/bin/python2.6 /share/apps/amber11/bin/MMPBSA -O -i decomp_tb_nm.in -o decomp_tb.dat -sp ../tryp_bpti_1000.top -cp ../GENR/tryp_bpti_nw.top -rp ../tryp_nw.top -lp ../bpti_nw.top -y ../tryp_bpti_1000.trj -do decomp_tryp_bpti.dat
> File "/share/apps/amber11/bin/MMPBSA", line 2
> if [ -z $AMBERHOME ]; then
> ^
> Do you understand it?
> Thanks for your help,
> Rami
>
> On Aug 22, 2011, at 11:27 AM, Seungyeul Yoo wrote:
>
> Hi Rami,
>
> I think you should use the executable named "MMPBSA" not "MMPBSA.py" for serial node job.
>
> For parallel, MMPBSA.MPI should be used.
>
> MMPBSA called another executable in the path of $AMBERHOME/AmberTools/src/mmpbsa_py/.
>
> I am not sure your problem is caused by this, but that is the right way to call the executables for MMPBSA calculations.
>
> Best regards,
>
> Seungyeul Yoo
>
> On Aug 21, 2011, at 10:23 AM, Osman, Roman wrote:
>
> Ray and MJ,
> I am back from vacation and I wanted to report the same problem I had before (on a different system) with some additional information.
> I want to describe briefly what is the setup:
> I have conducted a 50 ns simulations of a complex between trypsin and bpti. with ptraj I extracted 10000 snapshots with 1000 waters around the protein after centering imaging and rms fitting. The trajectory is written without box information. I then wanted to use this to compute the interaction energy with MMPBSA_py. The input to my first attempt was:
> &general
> verbose=2, strip_mdcrd=1, strip_mask=":WAT",
> entropy=0, startframe=1000, endframe=10000, interval=1000
> /
> &decomp
> idecomp=2, dec_verbose=3,
> /
> &gb
> igb=5, saltcon=0.150
> /
> &pb
> istrng=0.150
> /
> stripping all the waters and sampling every 1000 frames for 10 snapshots.
> the gb calculation works fine but the pb calculation works OK for the receptor but stops for the ligand and the complex with the following messages:
> for the _MMPBSA_ligand_pb.mdout:
> minimizing coord set # 7
> PB Bomb in assignlvlset(): no atmsas 36 -1 20
> 38 1 22 -2
> 38 1 22 -2
> 38 1 22 -2
> 38 1 22 -2
> 38 1 22 -1
> 38 1 22 1
> 38 1 22 -2
> PB Bomb in assignlvlset(): illegal insas flag 36 -1 20 -4
>
> and for the _MMPBSA_complex_pb.mdout:
> minimizing coord set # 7
> PB Bomb in assignlvlset(): no atmsas 35 -1 35
> 37 1 37 -2
> 37 1 37 -2
> 37 1 37 -2
> 37 1 37 -2
> 37 1 37 -1
> 37 1 37 1
> 37 1 37 -2
> PB Bomb in assignlvlset(): illegal insas flag 35 -1 35 -4
>
> I don't know the meaning of these numbers so it was difficult to trace back to the origin of the error although it seemed to mee that it has to do with the assignment of the dielectric boundaries.
> Since it seemed that the problem may be due to the coordinates of the ligand, I decided to determine at which point in the trajectory this happens by repeating the calculation with a finer interval. The input now is:
> &general
> verbose=2, strip_mdcrd=1, strip_mask=":WAT",
> entropy=0, startframe=6600, endframe=7500, interval=10
> /
> &decomp
> idecomp=2, dec_verbose=3,
> /
> &gb
> igb=5, saltcon=0.150
> /
> &pb
> istrng=0.150
> /
> As you can see it's al the same except the interval=10 and the range (startframe and endframe) brackets the #7 frame from the previous calculations.
> To my surprise the entire calculation for the 91 frames finished normally.
>
> The script I am using is as follows:
> #!/bin/bash
> #PBS -N MM_ALL
> #PBS -j oe -V
> #PBS -q serial_std
> #PBS -l select=1:ncpus=1
> #PBS -m e
>
> export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/share/apps/intel/lib/intel64
>
> cd $PBS_O_WORKDIR
>
> MMPBSA=/share/apps/amber11/bin/MMPBSA.py
>
> PYTHON="/share/apps/amber11/bin/python2.6"
>
> SUB="$PYTHON $MMPBSA -O -i decomp_tb_nm.in -o decomp_tb.dat -sp ../tryp_bpti_1000.top -cp ../GENR/tryp_bpti_nw.top -rp ../tryp_nw.top -lp ../bpti_nw.top -y ./tryp_bpti_1000.trj -do decomp_tryp_bpti.dat"
> echo $SUB
> $SUB
>
> Perhaps someone can disentangle this mystery.
> Thanks for your help.
> Rami
>
> On Aug 2, 2011, at 12:08 PM, Ray Luo, Ph.D. wrote:
>
> Let me first forward this to the mailing list for the sake of record keeping ...
>
> Ray
>
>
> ---------- Forwarded message ----------
> From: MengJuei Hsieh <mengjueh.uci.edu<mailto:mengjueh.uci.edu>>
> Date: Tue, Aug 2, 2011 at 8:48 AM
> Subject: Re: [AMBER] Problem with MMPBSA.py
> To: "Ray Luo, Ph.D." <ray.luo.uci.edu<mailto:ray.luo.uci.edu>>, Roman Osman <roman.osman.mssm.edu<mailto:roman.osman.mssm.edu>>
>
>
> Hi,
>
> I got some error in normal mode on our linux server, but the PBSA
> calculation did come through. So I suggest to checkout if PBSA/sander/nab
> are updated and make sure that pbsa, leap, ptraj, nab, mmpbsa_py, and sander
> are rebuilt after patches.
>
> Also attached after the mail is the log I had with normal mode errors.
>
> Best,
> --
> Mengjuei Hsieh, Molecular Biology & Biochem, Univ. of California Irvine.
>
>
> From: "Ray Luo, Ph.D." <ray.luo.uci.edu<mailto:ray.luo.uci.edu>>
> Date: Mon, 1 Aug 2011 17:48:04 -0700
> To: Roman Osman <roman.osman.mssm.edu<mailto:roman.osman.mssm.edu>>
>
> Rami,
>
> MJ is running your job, it's slow ... but the patched code seems to be
> working on Mac ... MJ is running it on Linux right now ...
>
> ----
> MMPBSA -O -i decomp_lig.in -o decomp_lig.dat -sp ./cbp_ro
> 5_200_py.top -cp ./cbp_ro5_nw_py.top -rp ./cbp_3dwy_py.top -lp ./ro5_py.top
> -y .
> /cbp_ro5_200.trj -do cbp_ror3_decnw.dat
> Reading command-line arguments and input files...
> Loading and checking parameter files for compatibility...
> ptraj found! Using /home/mjhsieh/amber11/bin/ptraj
> sander found! Using /home/mjhsieh/amber11/bin/sander for GB calculations
> sander found! Using /home/mjhsieh/amber11/bin/sander for PB calculations
> nmode program found! Using /home/mjhsieh/amber11/bin/mmpbsa_py_nabnmode
> Preparing trajectories for simulation...100 frames were read in and
> processed by ptraj for use in calculation.
>
> Beginning GB calculations with sander...
> calculating complex contribution...
> calculating receptor contribution...
> calculating ligand contribution...
>
> Beginning PB calculations with sander...
> calculating complex contribution...
> calculating receptor contribution...
> calculating ligand contribution...
> Beginning nmode calculations with mmpbsa_py_nabnmode...
> Calculating normal modes for 3 frames
>
> calculating complex contribution for frame 0
> calculating receptor contribution for frame 0
> calculating ligand contribution for frame 0
> calculating complex contribution for frame 1
> calculating receptor contribution for frame 1
> calculating ligand contribution for frame 1
> calculating complex contribution for frame 2
> calculating receptor contribution for frame 2
> calculating ligand contribution for frame 2
> Traceback (most recent call last):
> File "/home/mjhsieh/amber11/AmberTools/src/mmpbsa_py/MMPBSA.py", line
> 1343, in <module>
> outfile.write(str(nmodenorm))
> File "MMPBSA_mods/amberoutputs.py", line 2263, in __str__
> File "MMPBSA_mods/amberoutputs.py", line 2302, in AvgStdev
> File "MMPBSA_mods/amberoutputs.py", line 2319, in _tot_stdevs
> IndexError: list index out of range
>
> Roman Osman
> roman.osman.mssm.edu<mailto:roman.osman.mssm.edu>
>
>
>
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>
>
> _______________________________________________
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> AMBER.ambermd.org<mailto:AMBER.ambermd.org>
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>
> Roman Osman
> Department of Structural and Chemical Biology
> Mount Sinai School of Medicine
> New York, NY 10029
> Tel: 212-659-8627
> Fax: 212-849-2456
> e-mail: roman.osman.mssm.edu<mailto:roman.osman.mssm.edu>
> http://atlas.physbio.mssm.edu/~osmanlab
>
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
--
Jan-Philip Gehrcke
PhD student
Structural Bioinformatics Group
Technische Universität Dresden
Biotechnology Center
Tatzberg 47/49
01307 Dresden, Germany
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Received on Mon Aug 22 2011 - 10:00:03 PDT
