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
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Received on Sat Aug 13 2016 - 01:30:02 PDT
