Re: [AMBER] error in mdcrd box coordinates during MMPBSA calculation from Jason Swails on 2016-08-23 (Amber Archive Aug 2016)

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 23 Aug 2016 12:25:45 -0400

You can also use "netcdf=1" in the &general section to get better error
messages.

Note that the error message you are getting often results because the
prmtop and mdcrd files do not match. But since the format of the MDCRD
file is so ambiguous, cpptraj has a hard time guessing whether the format
is correct or not.

With NetCDF, however, there is no ambiguity and cpptraj can emit more
helpful error messages.

At the end of the day, being able to run these kinds of calculations by
hand will help you better debug problems using the MMPBSA.py script (since
you will know what MMPBSA.py is doing at each step and where something
might be going wrong).

As the manual suggests, you should use MM/PBSA scripts only after you can
demonstrably run the calculations by hand first.

HTH,
Jason

On Mon, Aug 22, 2016 at 8:56 PM, JoAnne Babula <jbabula.umail.iu.edu> wrote:

> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>

-- 
Jason M. Swails
_______________________________________________
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http://lists.ambermd.org/mailman/listinfo/amber

Received on Tue Aug 23 2016 - 09:30:03 PDT