Hi Ray,
Jason pointed me to one of the intermediate output files and it turned out
that I had an error like
"
*PB Bomb in pb_aaradi(): No radius assigned...". I searched the amber
database of Q&A and found the solution to the problem.thanks,*
*Shashi*
On Wed, Sep 24, 2014 at 1:40 PM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:
> Shashi,
>
> Can you run it in serial mode, without MPI?
>
> All the best,
>
> Ray
> --
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Shashidhar N. Rao
3 SERINA DRIVE
PLAINSBORO
NEW JERSEY 08536 USA
shashidharr.gmail.com
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Received on Wed Sep 24 2014 - 11:30:03 PDT
