Hello Hai,
There are 79 atoms in the ligand, 3134 in the receptor, and 3213 in the
complex top files, which all add up correctly. I have viewed all mdcrd
files with their matching top files on VMD just now and I did notice that
the top files for the ligand and receptor alone that I generated with
anteMMPBSA do not match up with the mdcrd files, so I have replaced these
paths with the top files I originally generated with tleap (and checked via
VMD).
After changing the path of the topology files back to the original tleap
top files instead of the anteMMPBSA generate top files I have successfully
completed the free energy calculation. Thank you so much to everyone who
helped on this thread. Here is the script:
###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_nowat.top -cp GRL_INO_nowat.top -rp
native_nowat.top -lp LINO_nowat.top -y GRL_INO_nowat.mdcrd -yr
native_nowat.mdcrd -yl LINO_nowat.mdcrd >progress
On Mon, Aug 22, 2016 at 1:17 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> make sure the total atoms in complex (-cp) = n_atoms in receptor (-rp) +
> n_atoms in ligand (-lp).
>
> (use head -10 *.prmtop to see the n_atoms or use "parminfo" command in
> cpptraj)
>
> Try to visualize (e.g VMD) with your topology file and corresponding
> trajectory
>
> -cp with -y
> -rp with -yr
> -lp with -yl
>
> Hai
>
> On Mon, Aug 22, 2016 at 12:58 PM, JoAnne Babula <jbabula.umail.iu.edu>
> wrote:
>
> > Actually I think the *.mdcrd is for non-imaged mdcrd files. I am using
> the
> > -y -yl -yr inputs because I want to use a different mdcrd for the
> complex,
> > receptor, and ligand. To my understanding the -y designates the complex
> > mdcrd and since I am using nowat mdcrd for receptor and ligand
> trajectories
> > shouldn't the complex trajectory also be no water? If not, I can
> certainly
> > change the -y input to the solvated mdcrd of the complex and leave the
> > ligand and receptor mdcrd as no water.
> >
> > On Mon, Aug 22, 2016 at 12:40 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> >
> > > 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
> > > >
> > > _______________________________________________
> > > 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
_______________________________________________
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Received on Mon Aug 22 2016 - 18:00:02 PDT
