Hi Amy,
Yes, this is exactly the input I was looking for. However, when I tried to
run this, I got an error about 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.
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.
On Wed, Aug 10, 2016 at 11:34 AM, Amy Rice <arice3.hawk.iit.edu> wrote:
> Hi JoAnne,
> Have you looked at chapter 31 of the Amber manual? There is a section on
> calling MMPBSA.py from the command line that explains how to give MMPBSA
> multiple trajectories: -y for the complex trajectory, -yr to specify the
> receptor trajectory, and -yl to specify the ligand trajectory.
>
> On Wed, Aug 10, 2016 at 9:47 AM, JoAnne Babula <jbabula.umail.iu.edu>
> wrote:
>
> > Hello,
> >
> > I would like to calculate the binding and total free energy for a
> > complex using AMBER14, but I would like to use 3 separate simulations to
> do
> > so, one with the ligand alone, one with the protein alone, and one of the
> > complex. I need to use three separate trajectories because the protein I
> am
> > using undergoes a conformational change when bound by the ligand, so
> using
> > the complex simulation alone does not deliver an accurate assessment of
> > total free energy change. I am not certain how to specify that I would
> like
> > the MMPBSA program to use 3 separate mdcrd files.
> > I have also noticed the FEW.pl program may be able to separately
> > calculate free energy for each simulation, but FEW also requires that the
> > simulations be generated through its workflow, and since I already have
> the
> > 3 simulations I would like to use, I would like to avoid this extra
> effort.
> > Can you suggest a course of action? 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
> >
>
>
>
> --
> Amy Rice
> Ph.D. Student
> Physics Department
> Illinois Institute of Technology
> _______________________________________________
> 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 Wed Aug 10 2016 - 11:30:02 PDT
