Re: [AMBER] failure to run MMPBSA job...

From: Ray Luo, Ph.D. <ray.luo.uci.edu> Date: Wed, 24 Sep 2014 10:40:52 -0700

--
Ray Luo, Ph.D.
Professor,
Biochemistry, Molecular Biophysics, Chemical Physics,
Chemical and Biomedical Engineering
University of California, Irvine, CA 92697-3900
On Wed, Sep 24, 2014 at 8:13 AM, Shashidhar Rao <shashidharr.gmail.com> wrote:
> Hello Amber Gurus,
>
> i am unable to run MMPBSA.py script a set of Amber MD trajectory structures
> as the job dies with the following set of errors:
>
> =============== error output ===========
>
> /net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/main.py:604:
> UserWarning: ligand_mask overwritten with default
>
>   warnings.warn('ligand_mask overwritten with default\n')
> /net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/main.py:604:
> UserWarning: ligand_mask overwritten with default
>
>   warnings.warn('ligand_mask overwritten with default\n')
> /net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/main.py:604:
> UserWarning: ligand_mask overwritten with default
>
>   warnings.warn('ligand_mask overwritten with default\n')
> /net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/main.py:604:
> UserWarning: ligand_mask overwritten with default
>
>   warnings.warn('ligand_mask overwritten with default\n')
> /net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/main.py:604:
> UserWarning: ligand_mask overwritten with default
>
>   warnings.warn('ligand_mask overwritten with default\n')
> /net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/main.py:604:
> UserWarning: ligand_mask overwritten with default
>
>   warnings.warn('ligand_mask overwritten with default\n')
> /net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/main.py:604:
> UserWarning: ligand_mask overwritten with default
>
>   warnings.warn('ligand_mask overwritten with default\n')
> /net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/main.py:604:
> UserWarning: ligand_mask overwritten with default
>
>   warnings.warn('ligand_mask overwritten with default\n')
>   File "/home/snr49/source/amber/bin/MMPBSA.py.MPI", line 96, in ?
>   File "/home/snr49/source/amber/bin/MMPBSA.py.MPI", line 96, in ?
>   File "/home/snr49/source/amber/bin/MMPBSA.py.MPI", line 96, in ?
>   File "/home/snr49/source/amber/bin/MMPBSA.py.MPI", line 96, in ?
>   File "/home/snr49/source/amber/bin/MMPBSA.py.MPI", line 96, in ?
>   File "/home/snr49/source/amber/bin/MMPBSA.py.MPI", line 96, in ?
>   File "/home/snr49/source/amber/bin/MMPBSA.py.MPI", line 96, in ?
>   File "/home/snr49/source/amber/bin/MMPBSA.py.MPI", line 96, in ?
>     app.run_mmpbsa()
>   File "/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/main.py", line
> 218, in run_mmpbsa
>     app.run_mmpbsa()
>   File "/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/main.py", line
> 218, in run_mmpbsa
>     app.run_mmpbsa()
>   File "/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/main.py", line
> 218, in run_mmpbsa
>     self.calc_list.run(rank, self.stdout)
>   File "/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/calculation.py",
> line 79, in run
>     self.calc_list.run(rank, self.stdout)
>   File "/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/calculation.py",
> line 79, in run
>     self.calc_list.run(rank, self.stdout)
>   File "/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/calculation.py",
> line 79, in run
>     app.run_mmpbsa()
>   File "/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/main.py", line
> 218, in run_mmpbsa
>     self.calc_list.run(rank, self.stdout)
>   File "/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/calculation.py",
> line 79, in run
>     app.run_mmpbsa()
>   File "/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/main.py", line
> 218, in run_mmpbsa
>     self.calc_list.run(rank, self.stdout)
>   File "/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/calculation.py",
> line 79, in run
>     app.run_mmpbsa()
>   File "/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/main.py", line
> 218, in run_mmpbsa
>     app.run_mmpbsa()
>   File "/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/main.py", line
> 218, in run_mmpbsa
>     self.calc_list.run(rank, self.stdout)
>     self.calc_list.run(rank, self.stdout)
>   File "/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/calculation.py",
> line 79, in run
>   File "/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/calculation.py",
> line 79, in run
>     app.run_mmpbsa()
>   File "/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/main.py", line
> 218, in run_mmpbsa
>     self.calc_list.run(rank, self.stdout)
>   File "/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/calculation.py",
> line 79, in run
>     calc.run(rank, stdout=stdout, stderr=stderr)
>   File "/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/calculation.py",
> line 415, in run
>     raise CalcError('%s failed with prmtop %s!\n\t' % (self.program,
> CalcError: /home/shashi/amber/bin/sander failed with prmtop
> /home/shashi/HIV_AMBER/INDIA/SSSS/MMGBSA/1QBT_SSSS_COMPLEX.prmtop!
>
>
> Error occured on rank 1.
> Exiting. All files have been retained.
>     calc.run(rank, stdout=stdout, stderr=stderr)
>   File "/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/calculation.py",
> line 415, in run
>     raise CalcError('%s failed with prmtop %s!\n\t' % (self.program,
>     calc.run(rank, stdout=stdout, stderr=stderr)
>   File "/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/calculation.py",
> line 415, in run
> CalcError: /home/shashi/amber/bin/sander failed with prmtop
> /home/shashi/HIV_AMBER/INDIA/SSSS/MMGBSA/1QBT_SSSS_COMPLEX.prmtop!
>
>
> Error occured on rank 5.
> Exiting. All files have been retained.
>     raise CalcError('%s failed with prmtop %s!\n\t' % (self.program,
> CalcError: /home/shashi/amber/bin/sander failed with prmtop
> /home/shashi/HIV_AMBER/INDIA/SSSS/MMGBSA/1QBT_SSSS_COMPLEX.prmtop!
>
>
> Error occured on rank 3.
> Exiting. All files have been retained.
>     calc.run(rank, stdout=stdout, stderr=stderr)
>   File "/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/calculation.py",
> line 415, in run
>     raise CalcError('%s failed with prmtop %s!\n\t' % (self.program,
> CalcError: /home/shashi/amber/bin/sander failed with prmtop
> /home/shashi/HIV_AMBER/INDIA/SSSS/MMGBSA/1QBT_SSSS_COMPLEX.prmtop!
>
>
> Error occured on rank 0.
> Exiting. All files have been retained.
>     calc.run(rank, stdout=stdout, stderr=stderr)
>   File "/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/calculation.py",
> line 415, in run
>     raise CalcError('%s failed with prmtop %s!\n\t' % (self.program,
> CalcError: /home/shashi/amber/bin/sander failed with prmtop
> /home/shashi/HIV_AMBER/INDIA/SSSS/MMGBSA/1QBT_SSSS_COMPLEX.prmtop!
>
>
> Error occured on rank 7.
> Exiting. All files have been retained.
>     calc.run(rank, stdout=stdout, stderr=stderr)
>   File "/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/calculation.py",
> line 415, in run
>     raise CalcError('%s failed with prmtop %s!\n\t' % (self.program,
> CalcError: /home/shashi/amber/bin/sander failed with prmtop
> /home/shashi/HIV_AMBER/INDIA/SSSS/MMGBSA/1QBT_SSSS_COMPLEX.prmtop!
>
>
> Error occured on rank 4.
> Exiting. All files have been retained.
>     calc.run(rank, stdout=stdout, stderr=stderr)
>   File "/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/calculation.py",
> line 415, in run
>     raise CalcError('%s failed with prmtop %s!\n\t' % (self.program,
> CalcError: /home/shashi/amber/bin/sander failed with prmtop
> /home/shashi/HIV_AMBER/INDIA/SSSS/MMGBSA/1QBT_SSSS_COMPLEX.prmtop!
>
>
> Error occured on rank 2.
> Exiting. All files have been retained.
>     calc.run(rank, stdout=stdout, stderr=stderr)
>   File "/net/cottusp/u2/snr49/source/amber/bin/MMPBSA_mods/calculation.py",
> line 415, in run
>     raise CalcError('%s failed with prmtop %s!\n\t' % (self.program,
> CalcError: /home/shashi/amber/bin/sander failed with prmtop
> /home/shashi/HIV_AMBER/INDIA/SSSS/MMGBSA/1QBT_SSSS_COMPLEX.prmtop!
>
>
> Error occured on rank 6.
> Exiting. All files have been retained.
> ===============================================================================================
>
> the input file used looks like this:
>
> ========== input file ==================
>
> &general
>
>   startframe=1, endframe=99999, interval=1, verbose=2, keep_files=1,
>   ligand_mask=":199",
>
> /
>
> &pb
>     istrng=0.15, fillratio=4.0,
> /
>
> &decomp
>         idecomp=2, dec_verbose=3
> /
>
>
> ========= end of input file ===================
>
> the command used (after setting all the environment variables like
> AMBERHOME, PATH and LD_LIBRARY_PATH) was as follows:
>
> /home/snr49/source/amber/bin/mpirun -np 8 MMPBSA.py.MPI -O -i
> /home/shashi/HIV_AMBER/INDIA/SSSS/MMPBSA/mmpbsa_input -cp
> /home/shashi/HIV_AMBER/INDIA/SSSS/MMGBSA/1QBT_SSSS_COMPLEX.prmtop -rp
> /home/shashi/HIV_AMBER/INDIA/1QBT_proteinonly.prmtop -lp
> /home/shashi/HIV_AMBER/INDIA/SSSS/MMGBSA/1QBTLIGAND.prmtop -eo
> ENERGY_traj1_SSSS.csv -y 1QBT_dmp_SSSS_complex_collection1_NoSOLVENT.netcdf
> -o FINAL_SSSS_traj1_Results.dat -do FINAL_SSSS_traj1_DECOMP_MMPBSA.dat
>
> ==========================
>
> i also separately executed (successfully) a sander run for minimizing one
> of the trajectory structures with the parm topology file
> "/home/shashi/HIV_AMBER/INDIA/SSSS/MMGBSA/1QBT_SSSS_COMPLEX.prmtop".  Hence
> I am a little puzzled as to why the program would complain about the
> failure of sander with the topology file.  I may also add that earlier, I
> had successfully run MMGBSA calculations on the same trajectory.
>
> thanks for help in resolving this issue,
>
> Shashi Rao
>
> --
> Shashidhar N. Rao
> 3 SERINA DRIVE
> PLAINSBORO
> NEW JERSEY 08536 USA
>
> shashidharr.gmail.com
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