Hi,
I did try the mask and I am still getting the same error. To make sure I
ran a new short simulation and ran the analysis and I get this error:
Loading and checking parameter files for compatibility...
mmpbsa_py_energy found! Using
/usr/local/packages/amber12/amber12/bin/mmpbsa_py_energy
cpptraj found! Using /usr/local/packages/amber12/amber12/bin/cpptraj
Preparing trajectories for simulation...
Usage: /usr/local/packages/amber12/amber12/bin/cpptraj [-p <Top1>, -p
<Top2>, ...] [-i <Input>] [-debug <N>]
/usr/local/packages/amber12/amber12/bin/cpptraj <Top1> <Input>
Additional options:
--help, -help: print usage information and exit.
-V, --version: print version information and exit.
--defines: print list of defines used in compilation.
File "/usr/local/packages/amber14/bin/MMPBSA.py", line 95, in <module>
app.file_setup()
File "/usr/local/packages/amber14/amber14/bin/MMPBSA_mods/main.py", line
156, in file_setup
self.mpi_size, str(external_progs['cpptraj']), self.pre)
File "/usr/local/packages/amber14/amber14/bin/MMPBSA_mods/make_trajs.py",
line 59, in make_trajectories
traj = Trajectory(FILES.solvated_prmtop, FILES.mdcrd, cpptraj)
File "/usr/local/packages/amber14/amber14/bin/MMPBSA_mods/make_trajs.py",
line 467, in __init__
self.Query()
File "/usr/local/packages/amber14/amber14/bin/MMPBSA_mods/make_trajs.py",
line 609, in Query
raise TrajError('Could not find number of frames in ' + traj)
TrajError: Could not find number of frames in MMPBSA.mdcrd
Exiting. All files have been retained.
the main problem seems to be with the trajectories that I make. I usually
save the trajectories in netcdf format. Does that cause this issue?
Regards,
Maryam
On Wed, Sep 28, 2016 at 10:19 PM, Dwight McGee <dwight.mcgee.gmail.com>
wrote:
> Hi,
>
> Try specifying both receptor_mask=":1-614,662-669" and
> ligand_mask=":615-661" in your mmpba.py input.
>
> cheers,
> Dwight
>
> On Wed, Sep 28, 2016 at 9:06 AM, maryam azimzadehirani <
> maryamai1988.gmail.com> wrote:
>
> > Dear Amber users,
> > I am trying to calculate ligand-receptor binding energy. my receptor is
> > glycosylated. I generated the initial topology file with this order: 1.
> > Receptor 2.ligand 3.glycans. Then I ran simulation.
> >
> > Now that I am trying to run binding energy calculation, I am getting this
> > error:
> > Reading command-line arguments and input files...
> > Loading and checking parameter files for compatibility...
> > PrmtopError: Couldn't predict mask from topology files!
> > Your ligand residues must be sequential in your complex.
> > There are likely problems with your topology files if this is not the
> case.
> > Exiting. All files have been retained.
> >
> > my input command line is:
> > MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp com_sol.prmtop
> > -cp EGF_EGFR_no_wat.prmtop -rp EGFR_gly_no_wat.prmtop -lp
> EGF_no_wat.prmtop
> > -y *.mdcrd
> >
> > where in the input file I specify the mask for the receptor residues as:
> > receptor_mask=:1-614,662-669
> >
> > Can you please guide me on how to fix this issue? Is this due to the way
> > that I made the complex topology? or there is some other mistake in my
> > calculations?
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> T. Dwight McGee Jr.
>
> dwight.mcgee.gmail.com
>
> "Problems cannot be solved at the same level of awareness that created
> them."
> Albert Einstein
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sun Oct 02 2016 - 18:00:03 PDT
