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
Received on Thu Aug 11 2016 - 12:00:04 PDT
