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
>
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Received on Fri Aug 12 2016 - 12:00:04 PDT
