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
Received on Mon Aug 22 2016 - 09:00:04 PDT
