Hi,
I think the *.mdcrd (prod.mdcrd) in the tutorial is for solvated trajectory.
Hai
On Mon, Aug 22, 2016 at 11:54 AM, JoAnne Babula <jbabula.umail.iu.edu>
wrote:
> Per the original command line in Amber tutorial 3 section 3.3, -sp input
> calls for the solvated top of the complex.
> $AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -sp ras-raf_solvated.prmtop -cp
> rasraf.prmtop -rp ras.prmtop -lp raf.prmtop -y *.mdcrd -mc
> rasraf_mutant.prmtop -mr ras_mutant.prmtop
>
> from: http://ambermd.org/tutorials/advanced/tutorial3/py_script/
> section3.htm
> The -cp input is the complex with solvate removed. I will attempt to run
> the job without the -sp input if you think that will solve the issue.
>
>
>
> On Mon, Aug 22, 2016 at 11:38 AM, Nhai <nhai.qn.gmail.com> wrote:
>
> >
> > No I meant that in the command line.
> >
> > Hai
> >
> > > On Aug 22, 2016, at 11:33 AM, JoAnne Babula <jbabula.umail.iu.edu>
> > wrote:
> > >
> > > Hello Nhai,
> > >
> > > The solvated top are per request of Bilal:
> > >
> > > JoAnne,
> > >
> > > Can you attach your solvated prmtop, so that I can check if i can
> > reproduce
> > > the error? How big is your trajectory? is it possible to try it with
> few
> > > frames only. Or try the same step with serial version of mmpbsa.py, see
> > if
> > > the issue is resolved.
> > >
> > >
> > >
> > > I am assuming he is going to run a strip on the water himself and try
> to
> > re
> > > produce my error message.
> > >
> > >> On Mon, Aug 22, 2016 at 11:31 AM, Nhai <nhai.qn.gmail.com> wrote:
> > >>
> > >> All of you trajectories are nowat, so what is GRL_INO_solvate.top for?
> > >>
> > >> Hai
> > >>
> > >>>> On Aug 22, 2016, at 10:19 AM, JoAnne Babula <jbabula.umail.iu.edu>
> > >>> wrote:
> > >>>
> > >>> Hi Bilal,
> > >>>
> > >>> I have attempted to run the free energy calculation with your
> > suggestions
> > >>> and received the following error messages:
> > >>>
> > >>> 1. With serial MMPBSA.py:
> > >>>
> > >>>
> > >>> Error: In GRL_INO_nowat.mdcrd, expect only 3 or 6 box coords, got 4
> > >>> Error: Box line=[ -17.791 15.073 -3.686 -19.485
> > >>> ]
> > >>> Error: In GRL_INO_nowat.mdcrd, expect only 3 or 6 box coords, got 4
> > >>> Error: Box line=[ -17.791 15.073 -3.686 -19.485
> > >>> ]
> > >>> Error: Could not set up GRL_INO_nowat.mdcrd for reading.
> > >>> Error: Could not set up input trajectory 'GRL_INO_nowat.mdcrd'.
> > >>> Error: In GRL_INO_nowat.mdcrd, expect only 3 or 6 box coords, got 4
> > >>> Error: Box line=[ -17.791 15.073 -3.686 -19.485
> > >>> ]
> > >>> Error: Could not set up GRL_INO_nowat.mdcrd for reading.
> > >>> Error: Could not set up input trajectory 'GRL_INO_nowat.mdcrd'.
> > >>> Error: Could not set up GRL_INO_nowat.mdcrd for reading.
> > >>> Error: Could not set up input trajectory 'GRL_INO_nowat.mdcrd'.
> > >>> Error: In GRL_INO_nowat.mdcrd, expect only 3 or 6 box coords, got 4
> > >>> Error: Box line=[ -17.791 15.073 -3.686 -19.485
> > >>> ]
> > >>> Error: Could not set up GRL_INO_nowat.mdcrd for reading.
> > >>> Error: Could not set up input trajectory 'GRL_INO_nowat.mdcrd'.
> > >>> File "/N/soft/rhel6/amber/intel/mpi/14/amber14/bin/MMPBSA.py", line
> > >> 103,
> > >>> in <module>
> > >>> "/N/soft/rhel6/amber/intel/mpi/14/amber14/bin/MMPBSA.py", line 103,
> in
> > >>> <module>
> > >>> File "/N/soft/rhel6/amber/intel/mpi/14/amber14/bin/MMPBSA.py", line
> > >> 103,
> > >>> in <module>
> > >>> app.file_setup()
> > >>> File
> > >>> "/N/soft/rhel6/amber/intel/mpi/14/amber14/lib/python2.7/
> > >> site-packages/MMPBSA_mods/main.py",
> > >>> line 156, in file_setup
> > >>> app.file_setup()
> > >>> File
> > >>> "/N/soft/rhel6/amber/intel/mpi/14/amber14/lib/python2.7/
> > >> site-packages/MMPBSA_mods/main.py",
> > >>> line 156, in file_setup
> > >>> app.file_setup()
> > >>> File
> > >>> "/N/soft/rhel6/amber/intel/mpi/14/amber14/lib/python2.7/
> > >> site-packages/MMPBSA_mods/main.py",
> > >>> line 156, in file_setup
> > >>> File "/N/soft/rhel6/amber/intel/mpi/14/amber14/bin/MMPBSA.py", line
> > >> 103,
> > >>> in <module>
> > >>> app.file_setup()
> > >>> File
> > >>> "/N/soft/rhel6/amber/intel/mpi/14/amber14/lib/python2.7/
> > >> site-packages/MMPBSA_mods/main.py",
> > >>> line 156, in file_setup
> > >>> self.mpi_size, str(external_progs['cpptraj']), self.pre)
> > >>> File
> > >>> "/N/soft/rhel6/amber/intel/mpi/14/amber14/lib/python2.7/
> > >> site-packages/MMPBSA_mods/make_trajs.py",
> > >>> line 59, in make_trajectories
> > >>> self.mpi_size, str(external_progs['cpptraj']), self.pre)
> > >>> File
> > >>> "/N/soft/rhel6/amber/intel/mpi/14/amber14/lib/python2.7/
> > >> site-packages/MMPBSA_mods/make_trajs.py",
> > >>> line 59, in make_trajectories
> > >>> self.mpi_size, str(external_progs['cpptraj']), self.pre)
> > >>> File
> > >>> "/N/soft/rhel6/amber/intel/mpi/14/amber14/lib/python2.7/
> > >> site-packages/MMPBSA_mods/make_trajs.py",
> > >>> line 59, in make_trajectories
> > >>> self.mpi_size, str(external_progs['cpptraj']), self.pre)
> > >>> File
> > >>> "/N/soft/rhel6/amber/intel/mpi/14/amber14/lib/python2.7/
> > >> site-packages/MMPBSA_mods/make_trajs.py",
> > >>> line 59, in make_trajectories
> > >>> traj = Trajectory(FILES.solvated_prmtop, FILES.mdcrd, cpptraj)
> > >>> File
> > >>> "/N/soft/rhel6/amber/intel/mpi/14/amber14/lib/python2.7/
> > >> site-packages/MMPBSA_mods/make_trajs.py",
> > >>> line 467, in __init__
> > >>> self.Query()
> > >>> File
> > >>> "/N/soft/rhel6/amber/intel/mpi/14/amber14/lib/python2.7/
> > >> site-packages/MMPBSA_mods/make_trajs.py",
> > >>> line 602, in Query
> > >>> raise TrajError('%s failed when querying %s' % (self.exe, traj))
> > >>> TrajError: /N/soft/rhel6/amber/intel/mpi/14/amber14/bin/cpptraj
> failed
> > >> when
> > >>> querying GRL_INO_nowat.mdcrd
> > >>> Exiting. All files have been retained.
> > >>> traj = Trajectory(FILES.solvated_prmtop, FILES.mdcrd, cpptraj)
> > >>> File
> > >>> "/N/soft/rhel6/amber/intel/mpi/14/amber14/lib/python2.7/
> > >> site-packages/MMPBSA_mods/make_trajs.py",
> > >>> line 467, in __init__
> > >>> self.Query()
> > >>> File
> > >>> "/N/soft/rhel6/amber/intel/mpi/14/amber14/lib/python2.7/
> > >> site-packages/MMPBSA_mods/make_trajs.py",
> > >>> line 602, in Query
> > >>> raise TrajError('%s failed when querying %s' % (self.exe, traj))
> > >>> TrajError: /N/soft/rhel6/amber/intel/mpi/14/amber14/bin/cpptraj
> failed
> > >> when
> > >>> querying GRL_INO_nowat.mdcrd
> > >>> Exiting. All files have been retained.
> > >>> traj = Trajectory(FILES.solvated_prmtop, FILES.mdcrd, cpptraj)
> > >>> File
> > >>> "/N/soft/rhel6/amber/intel/mpi/14/amber14/lib/python2.7/
> > >> site-packages/MMPBSA_mods/make_trajs.py",
> > >>> line 467, in __init__
> > >>> self.Query()
> > >>> File
> > >>> "/N/soft/rhel6/amber/intel/mpi/14/amber14/lib/python2.7/
> > >> site-packages/MMPBSA_mods/make_trajs.py",
> > >>> line 602, in Query
> > >>> raise TrajError('%s failed when querying %s' % (self.exe, traj))
> > >>> TrajError: /N/soft/rhel6/amber/intel/mpi/14/amber14/bin/cpptraj
> failed
> > >> when
> > >>> querying GRL_INO_nowat.mdcrd
> > >>> Exiting. All files have been retained.
> > >>> traj = Trajectory(FILES.solvated_prmtop, FILES.mdcrd, cpptraj)
> > >>> File
> > >>> "/N/soft/rhel6/amber/intel/mpi/14/amber14/lib/python2.7/
> > >> site-packages/MMPBSA_mods/make_trajs.py",
> > >>> line 467, in __init__
> > >>> self.Query()
> > >>> File
> > >>> "/N/soft/rhel6/amber/intel/mpi/14/amber14/lib/python2.7/
> > >> site-packages/MMPBSA_mods/make_trajs.py",
> > >>> line 602, in Query
> > >>> raise TrajError('%s failed when querying %s' % (self.exe, traj))
> > >>> TrajError: /N/soft/rhel6/amber/intel/mpi/14/amber14/bin/cpptraj
> failed
> > >> when
> > >>> querying GRL_INO_nowat.mdcrd
> > >>> Exiting. All files have been retained.
> > >>>
> > >>>
> > >>> and the input file being:
> > >>> ###Input file for running PB and GB####
> > >>> cat <<eof > mmpbsa.in
> > >>> Input file for running PB and GB
> > >>> &general
> > >>> startframe=20000, interval=80, endframe=120000, keep_files=2,
> > >>> /
> > >>> &gb
> > >>> igb=2, saltcon=0.100,
> > >>> /
> > >>> &pb
> > >>> istrng=0.100,
> > >>> /
> > >>> eof
> > >>> mpirun -n 4 MMPBSA.py -O -i mmpbsa.in -o pbsa_karst.dat -sp
> > >>> ../../../../../INO/sim1/PREP/GRL_INO_solvate.top -cp
> > >> top/GRL_INO_nowat.top
> > >>> -rp top/native_nowat.top -lp top/LINO_nowat.top -y
> GRL_INO_nowat.mdcrd
> > >> -yr
> > >>> native_nowat.mdcrd -yl LINO_nowat.mdcrd >progress
> > >>> ~
> > >>>
> > >>>
> > >>> 2. With smaller mdcrd files of 20,000 frames instead of 120,000:
> > >>>
> > >>> File "/N/soft/rhel6/amber/intel/mpi/14/amber14/bin/MMPBSA.py.MPI",
> > line
> > >>> 103, in <module>
> > >>> app.file_setup()
> > >>> File
> > >>> "/N/soft/rhel6/amber/intel/mpi/14/amber14/lib/python2.7/
> > >> site-packages/MMPBSA_mods/main.py",
> > >>> line 156, in file_setup
> > >>> self.mpi_size, str(external_progs['cpptraj']), self.pre)
> > >>> File
> > >>> "/N/soft/rhel6/amber/intel/mpi/14/amber14/lib/python2.7/
> > >> site-packages/MMPBSA_mods/make_trajs.py",
> > >>> line 76, in make_trajectories
> > >>> raise MMPBSA_Error('Must have at least as many frames as
> > processors!')
> > >>> MMPBSA_Error: Must have at least as many frames as processors!
> > >>> Error occured on rank 0.
> > >>> Exiting. All files have been retained.
> > >>>
> > >>>
> > >>>
> > >>>
> > >>>
> > >>>
> > >>> On Sat, Aug 13, 2016 at 4:11 AM, Bilal Nizami <
> > nizamibilal1064.gmail.com
> > >>>
> > >>> wrote:
> > >>>
> > >>>> JoAnne,
> > >>>>
> > >>>> Can you attach your solvated prmtop, so that I can check if i can
> > >> reproduce
> > >>>> the error? How big is your trajectory? is it possible to try it with
> > few
> > >>>> frames only. Or try the same step with serial version of mmpbsa.py,
> > see
> > >> if
> > >>>> the issue is resolved.
> > >>>>
> > >>>> Regards,
> > >>>>
> > >>>> 2016-08-12 20:49 GMT+02:00 Hai Nguyen <nhai.qn.gmail.com>:
> > >>>>
> > >>>>> you can try to follow old thread first.
> > >>>>>
> > >>>>> https://www.google.com/search?q=expect+only+3+or+6+box+
> > >>>>> coords&ie=utf-8&oe=utf-8#q=expect+only+3+or+6+box+coords&tbas=0
> > >>>>>
> > >>>>> PS: You should always use netcdf format.
> > >>>>>
> > >>>>> Hai
> > >>>>>
> > >>>>> On Fri, Aug 12, 2016 at 2:41 PM, JoAnne Babula <
> jbabula.umail.iu.edu
> > >
> > >>>>> wrote:
> > >>>>>
> > >>>>>> Okay, my apologies, I have no re-run the script with the @
> > designation
> > >>>>> and
> > >>>>>> produced the 3 respective topologies. However, I still received
> the
> > >>>> same
> > >>>>>> error concerning the box coordinates:
> > >>>>>>
> > >>>>>> Error: In GRL_INO_nowat.mdcrd, expect only 3 or 6 box coords, got
> 4
> > >>>>>> Error: Box line=[ -17.791 15.073 -3.686 -19.485
> > >>>>>> ]
> > >>>>>> Error: Could not set up GRL_INO_nowat.mdcrd for reading.
> > >>>>>> Error: Could not set up input trajectory 'GRL_INO_nowat.mdcrd'.
> > >>>>>> File "/N/soft/rhel6/amber/intel/mpi/14/amber14/bin/MMPBSA.py.
> MPI",
> > >>>>> line
> > >>>>>> 103, in <module>
> > >>>>>> app.file_setup()
> > >>>>>> File
> > >>>>>> "/N/soft/rhel6/amber/intel/mpi/14/amber14/lib/python2.7/
> > >>>>>> site-packages/MMPBSA_mods/main.py",
> > >>>>>> line 156, in file_setup
> > >>>>>> self.mpi_size, str(external_progs['cpptraj']), self.pre)
> > >>>>>> File
> > >>>>>> "/N/soft/rhel6/amber/intel/mpi/14/amber14/lib/python2.7/
> > >>>>>> site-packages/MMPBSA_mods/make_trajs.py",
> > >>>>>> line 59, in make_trajectories
> > >>>>>> traj = Trajectory(FILES.solvated_prmtop, FILES.mdcrd, cpptraj)
> > >>>>>> File
> > >>>>>> "/N/soft/rhel6/amber/intel/mpi/14/amber14/lib/python2.7/
> > >>>>>> site-packages/MMPBSA_mods/make_trajs.py",
> > >>>>>> line 467, in __init__
> > >>>>>> self.Query()
> > >>>>>> File
> > >>>>>> "/N/soft/rhel6/amber/intel/mpi/14/amber14/lib/python2.7/
> > >>>>>> site-packages/MMPBSA_mods/make_trajs.py",
> > >>>>>> line 602, in Query
> > >>>>>> raise TrajError('%s failed when querying %s' % (self.exe, traj))
> > >>>>>> TrajError: /N/soft/rhel6/amber/intel/mpi/14/amber14/bin/cpptraj
> > >> failed
> > >>>>>> when
> > >>>>>> querying GRL_INO_nowat.mdcrd
> > >>>>>> Error occured on rank 0.
> > >>>>>> Exiting. All files have been retained.
> > >>>>>>
> > >>>>>>
> > >>>>>> Any other ideas?
> > >>>>>>
> > >>>>>>
> > >>>>>> On Fri, Aug 12, 2016 at 1:38 PM, JoAnne Babula <
> > jbabula.umail.iu.edu>
> > >>>>>> wrote:
> > >>>>>>
> > >>>>>>> The ligand is atoms 3135-3213. Water is 3124-39717.
> > >>>>>>>
> > >>>>>>> On Fri, Aug 12, 2016 at 1:34 PM, JoAnne Babula <
> > jbabula.umail.iu.edu
> > >>>>>
> > >>>>>>> wrote:
> > >>>>>>>
> > >>>>>>>> Hi Bilal,
> > >>>>>>>>
> > >>>>>>>> I have run the ante-MMPBSA.py script using the following on the
> > >>>>> command
> > >>>>>>>> line:
> > >>>>>>>>
> > >>>>>>>> ../../../soft/rhel6/amber/intel/mpi/14/amber14/bin/ante-
> MMPBSA.py
> > >>>> -p
> > >>>>>>>> ../../../../../../INO/sim1/PREP/GRL_INO_solvate.top -c
> > >>>>>>>> top/GRL_INO_nowat.top -r top/native_nowat.top -l
> > top/LINO_nowat.top
> > >>>> -s
> > >>>>>>>> 3214-39717 -m 3135-3213
> > >>>>>>>>
> > >>>>>>>>
> > >>>>>>>> It does not let me specify both -m and -n for the receptor and
> > >>>> ligand
> > >>>>> is
> > >>>>>>>> that correct? This script generated 3 identical topology files
> for
> > >>>> me
> > >>>>>>>> instead of writing and complex, receptor, and ligand topology
> > >>>>>> separately.
> > >>>>>>>> Have I typed something incorrectly? the -s is asking for the
> water
> > >>>>> atoms
> > >>>>>>>> only, correct? Thank you!
> > >>>>>>>>
> > >>>>>>>>
> > >>>>>>>> On Fri, Aug 12, 2016 at 3:15 AM, Bilal Nizami <
> > >>>>>> nizamibilal1064.gmail.com>
> > >>>>>>>> wrote:
> > >>>>>>>>
> > >>>>>>>>> Hi JoAnne,
> > >>>>>>>>>
> > >>>>>>>>> Try making the dry complex, receptor and ligand topology file
> > from
> > >>>>>>>>> solvated
> > >>>>>>>>> complex topology file using anteMMPBSA.
> > >>>>>>>>> It helped me sometime to avoid error with topology/trajectory
> > with
> > >>>>>>>>> MMPBSA.py. You can use following command:
> > >>>>>>>>>
> > >>>>>>>>> *ante-MMPBSA.py -p *GRL_INO_solvate*.top -c *GRL_INO_nowat.top*
> > -r
> > >>>> *
> > >>>>>>>>> native_nowat.top* -l *LINO_nowat.top * -s <atom mask> -m <atom
> > >>>> mask>*
> > >>>>>>>>>
> > >>>>>>>>> You can check amber manual for details of the ante-MMPBSA.py.
> > >>>>>>>>>
> > >>>>>>>>>
> > >>>>>>>>> Regards,
> > >>>>>>>>>
> > >>>>>>>>> 2016-08-11 20:49 GMT+02:00 Hai Nguyen <nhai.qn.gmail.com>:
> > >>>>>>>>>
> > >>>>>>>>>> I am not familiar enough with MMGBSA code so can not provide
> > >>>> useful
> > >>>>>>>>> debug
> > >>>>>>>>>> info.
> > >>>>>>>>>>
> > >>>>>>>>>> While waiting for other's feedback, you can try to upgrade to
> > >>>>>>>>> ambertools16:
> > >>>>>>>>>> http://ambermd.org/AmberTools16-get.html
> > >>>>>>>>>>
> > >>>>>>>>>> Hai
> > >>>>>>>>>>
> > >>>>>>>>>> On Thu, Aug 11, 2016 at 2:41 PM, JoAnne Babula <
> > >>>>> jbabula.umail.iu.edu
> > >>>>>>>
> > >>>>>>>>>> wrote:
> > >>>>>>>>>>
> > >>>>>>>>>>> Hi Hai,
> > >>>>>>>>>>>
> > >>>>>>>>>>> Yes cpptraj successfully reads the mdcrd. I can also use the
> > >>>>>>>>>>> GRL_INO_nowat.top to view the mdcrd with VMD.
> > >>>>>>>>>>>
> > >>>>>>>>>>> On Thu, Aug 11, 2016 at 2:32 PM, Hai Nguyen <
> nhai.qn.gmail.com
> > >>>>>
> > >>>>>>>>> wrote:
> > >>>>>>>>>>>
> > >>>>>>>>>>>> are you able to read GRL_INO_nowat.mdcrd with cpptraj?
> > >>>>>>>>>>>>
> > >>>>>>>>>>>> Hai
> > >>>>>>>>>>>>
> > >>>>>>>>>>>> On Thu, Aug 11, 2016 at 11:21 AM, JoAnne Babula <
> > >>>>>>>>> jbabula.umail.iu.edu>
> > >>>>>>>>>>>> wrote:
> > >>>>>>>>>>>>
> > >>>>>>>>>>>>> Hello,
> > >>>>>>>>>>>>>
> > >>>>>>>>>>>>> I am trying to run a free energy calculation using 3
> > >>>>>> trajectories
> > >>>>>>>>>> with
> > >>>>>>>>>>>>> MMPBSA. I received this error with the mdcrd for the
> > >>>> complex:
> > >>>>>>>>>>>>>
> > >>>>>>>>>>>>> Error: In GRL_INO_nowat.mdcrd, expect only 3 or 6 box
> > >>>> coords,
> > >>>>>>>>> got 4
> > >>>>>>>>>>>>> Error: Box line=[ -17.791 15.073 -3.686 -19.485
> > >>>>>>>>>>>>> ]
> > >>>>>>>>>>>>> Error: Could not set up GRL_INO_nowat.mdcrd for reading.
> > >>>>>>>>>>>>> Error: Could not set up input trajectory
> > >>>>> 'GRL_INO_nowat.mdcrd'.
> > >>>>>>>>>>>>> File "/N/soft/rhel6/amber/intel/mpi
> > >>>>>>>>> /14/amber14/bin/MMPBSA.py.MPI",
> > >>>>>>>>>>>> line
> > >>>>>>>>>>>>> 103, in <module>
> > >>>>>>>>>>>>> app.file_setup()
> > >>>>>>>>>>>>> File "/N/soft/rhel6/amber/intel/
> > >>>>>> mpi/14/amber14/lib/python2.7/
> > >>>>>>>>>>>>> site-packages/MMPBSA_mods/main.py", line 156, in
> > >>>> file_setup
> > >>>>>>>>>>>>> self.mpi_size, str(external_progs['cpptraj']),
> > >>>> self.pre)
> > >>>>>>>>>>>>> File "/N/soft/rhel6/amber/intel/
> > >>>>>> mpi/14/amber14/lib/python2.7/
> > >>>>>>>>>>>>> site-packages/MMPBSA_mods/make_trajs.py", line 59, in
> > >>>>>>>>>>> make_trajectories
> > >>>>>>>>>>>>> traj = Trajectory(FILES.solvated_prmtop, FILES.mdcrd,
> > >>>>>>>>> cpptraj)
> > >>>>>>>>>>>>> File "/N/soft/rhel6/amber/intel/
> > >>>>>> mpi/14/amber14/lib/python2.7/
> > >>>>>>>>>>>>> site-packages/MMPBSA_mods/make_trajs.py", line 467, in
> > >>>>>> __init__
> > >>>>>>>>>>>>> self.Query()
> > >>>>>>>>>>>>> File "/N/soft/rhel6/amber/intel/
> > >>>>>> mpi/14/amber14/lib/python2.7/
> > >>>>>>>>>>>>> site-packages/MMPBSA_mods/make_trajs.py", line 602, in
> > >>>> Query
> > >>>>>>>>>>>>> raise TrajError('%s failed when querying %s' %
> > >>>> (self.exe,
> > >>>>>>>>> traj))
> > >>>>>>>>>>>>> TrajError: /N/soft/rhel6/amber/intel/mpi/
> > >>>>>> 14/amber14/bin/cpptraj
> > >>>>>>>>>> failed
> > >>>>>>>>>>>>> when
> > >>>>>>>>>>>>> querying GRL_INO_nowat.mdcrd
> > >>>>>>>>>>>>> Error occured on rank 0.
> > >>>>>>>>>>>>> Exiting. All files have been retained.
> > >>>>>>>>>>>>>
> > >>>>>>>>>>>>>
> > >>>>>>>>>>>>>
> > >>>>>>>>>>>>> Do you know why this may have happened? Here is my input:
> > >>>>>>>>>>>>> ###Input file for running PB and GB####
> > >>>>>>>>>>>>> cat <<eof > mmpbsa.in
> > >>>>>>>>>>>>> Input file for running PB and GB
> > >>>>>>>>>>>>> &general
> > >>>>>>>>>>>>> startframe=20000, interval=80, endframe=120000,
> > >>>>>> keep_files=2,
> > >>>>>>>>>>>>> /
> > >>>>>>>>>>>>> &gb
> > >>>>>>>>>>>>> igb=2, saltcon=0.100,
> > >>>>>>>>>>>>> /
> > >>>>>>>>>>>>> &pb
> > >>>>>>>>>>>>> istrng=0.100,
> > >>>>>>>>>>>>> /
> > >>>>>>>>>>>>> eof
> > >>>>>>>>>>>>> mpirun -n 4 MMPBSA.py.MPI -O -i mmpbsa.in -o
> > >>>> pbsa_karst.dat
> > >>>>>> -sp
> > >>>>>>>>>>>>> ../../../../../INO/sim1/PREP/GRL_INO_solvate.top -cp
> > >>>>>>>>>>>>> ../../../../../INO/sim1/PREP/GRL_INO_nowat.top -rp
> > >>>>>>>>>>>>> ../../../../../Native/sim_1/PREP/native_nowat.top -lp
> > >>>>>>>>>>>>> ../../PREP/LINO_nowat.top -y GRL_INO_nowat.mdcrd -yr
> > >>>>>>>>>> native_nowat.mdcrd
> > >>>>>>>>>>>> -yl
> > >>>>>>>>>>>>> LINO_nowat.mdcrd >progress
> > >>>>>>>>>>>>>
> > >>>>>>>>>>>>>
> > >>>>>>>>>>>>>
> > >>>>>>>>>>>>> Thank you so much.
> > >>>>>>>>>>>>>
> > >>>>>>>>>>>>> --
> > >>>>>>>>>>>>> Very Respectfully,
> > >>>>>>>>>>>>>
> > >>>>>>>>>>>>> JoAnne J Babula
> > >>>>>>>>>>>>> Ph.D. Candidate, IUSM, Dept. of Pharmacology
> > >>>>>>>>>>>>> U.S. Army, 1LT, MS
> > >>>>>>>>>>>>> _______________________________________________
> > >>>>>>>>>>>>> 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
> > >>>>>>>>>>>
> > >>>>>>>>>>>
> > >>>>>>>>>>>
> > >>>>>>>>>>> --
> > >>>>>>>>>>> Very Respectfully,
> > >>>>>>>>>>>
> > >>>>>>>>>>> JoAnne J Babula
> > >>>>>>>>>>> Ph.D. Candidate, IUSM, Dept. of Pharmacology
> > >>>>>>>>>>> U.S. Army, 1LT, MS
> > >>>>>>>>>>> _______________________________________________
> > >>>>>>>>>>> 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
> > >>>>>>>>>
> > >>>>>>>>>
> > >>>>>>>>>
> > >>>>>>>>> --
> > >>>>>>>>> *Bilal Nizami*
> > >>>>>>>>> School of Health Sciences
> > >>>>>>>>> University of KwaZulu-Natal
> > >>>>>>>>> Durban
> > >>>>>>>>> 4000
> > >>>>>>>>> South Africa
> > >>>>>>>>>
> > >>>>>>>>> Linkedin: za.linkedin.com/pub/bilal-nizami/49/673/790/
> > >>>>>>>>> Email: 214573074.stu.ukzn.ac.za
> > >>>>>>>>> _______________________________________________
> > >>>>>>>>> AMBER mailing list
> > >>>>>>>>> AMBER.ambermd.org
> > >>>>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
> > >>>>>>>>
> > >>>>>>>>
> > >>>>>>>>
> > >>>>>>>> --
> > >>>>>>>> Very Respectfully,
> > >>>>>>>>
> > >>>>>>>> JoAnne J Babula
> > >>>>>>>> Ph.D. Candidate, IUSM, Dept. of Pharmacology
> > >>>>>>>> U.S. Army, 1LT, MS
> > >>>>>>>
> > >>>>>>>
> > >>>>>>>
> > >>>>>>> --
> > >>>>>>> Very Respectfully,
> > >>>>>>>
> > >>>>>>> JoAnne J Babula
> > >>>>>>> Ph.D. Candidate, IUSM, Dept. of Pharmacology
> > >>>>>>> U.S. Army, 1LT, MS
> > >>>>>>
> > >>>>>>
> > >>>>>>
> > >>>>>> --
> > >>>>>> Very Respectfully,
> > >>>>>>
> > >>>>>> JoAnne J Babula
> > >>>>>> Ph.D. Candidate, IUSM, Dept. of Pharmacology
> > >>>>>> U.S. Army, 1LT, MS
> > >>>>>> _______________________________________________
> > >>>>>> 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
> > >>>>
> > >>>>
> > >>>>
> > >>>> --
> > >>>> *Bilal Nizami*
> > >>>> School of Health Sciences
> > >>>> University of KwaZulu-Natal
> > >>>> Durban
> > >>>> 4000
> > >>>> South Africa
> > >>>>
> > >>>> Linkedin: za.linkedin.com/pub/bilal-nizami/49/673/790/
> > >>>> Email: 214573074.stu.ukzn.ac.za
> > >>>> _______________________________________________
> > >>>> AMBER mailing list
> > >>>> AMBER.ambermd.org
> > >>>> http://lists.ambermd.org/mailman/listinfo/amber
> > >>>
> > >>>
> > >>>
> > >>> --
> > >>> Very Respectfully,
> > >>>
> > >>> JoAnne J Babula
> > >>> Ph.D. Candidate, IUSM, Dept. of Pharmacology
> > >>> U.S. Army, 1LT, MS
> > >>> _______________________________________________
> > >>> 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
> > >
> > >
> > >
> > > --
> > > Very Respectfully,
> > >
> > > JoAnne J Babula
> > > Ph.D. Candidate, IUSM, Dept. of Pharmacology
> > > U.S. Army, 1LT, MS
> > > _______________________________________________
> > > 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
> >
>
>
>
> --
> Very Respectfully,
>
> JoAnne J Babula
> Ph.D. Candidate, IUSM, Dept. of Pharmacology
> U.S. Army, 1LT, MS
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
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Received on Mon Aug 22 2016 - 10:00:02 PDT
