On Tue, Sep 2, 2014 at 3:41 PM, Renato Freitas <renatoffs.gmail.com> wrote:
> Yes coordinates for the wild-type complex is complex.inpcrd. Also, the file
> _MMPBSA_complex.mdcrd.0 was generated, and I didn't have problem to open
> this file with the complex.prmtop in VMD. Actually, the
> files _MMPBSA_complex.mdcrd.0 and complex.inpcrd when opened in VMD look
> exactly the same.
> Any idea on what's is wrong?
>
Not yet. Does it work with AmberTools 14?
>
> thanks,
>
> Renato
>
>
> On Tue, Sep 2, 2014 at 3:03 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
> > On Tue, 2014-09-02 at 13:12 -0400, Renato Freitas wrote:
> > > I am trying to run an alanine scaning (single point) on a
> protein-peptide
> > > complex, where I am mutating the ligand. I generated the topology file
> > for
> > > wild ligand, receptor and complex as well as for the corresponding
> > mutants.
> > > Then I tried to rung MMPBSA.py using the command bellow:
> > >
> > > MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA_A6 -cp
> complex.prmtop
> > -rp
> > > receptor.prmtop -lp ligand.prmtop -mc mutant_complex.prmtop -ml
> > > mutant_ligand.prmtop -y complex.inpcrd
> > >
> > > but I got this error:
> > >
> > > Loading and checking parameter files for compatibility...
> > > mmpbsa_py_energy found! Using /opt/amber12/bin/mmpbsa_py_
> > > energy
> > > cpptraj found! Using /opt/amber12/bin/cpptraj
> > > Preparing trajectories for simulation...
> > > Mutating trajectories...
> > > TypeError: not all arguments converted during string formatting
> > > Exiting. All files have been retained.
> > >
> > > I checked all the topology file and it seems that everything is
> correct.
> > I
> > > also didn't got any error running tleap. Any help will be appreciated.
> >
> > complex.inpcrd is the inpcrd file for the wild-type complex, correct?
> >
> > Did a _MMPBSA_complex.mdcrd.0 file get generated by any chance? What
> > happens if you visualize that with the complex prmtop?
> >
> > Also, I would suggest updating to the latest version of AmberTools 14,
> > since at least one bug in alanine scanning has been fixed since then
> > (although this problem looks different).
> >
> > HTH,
> > Jason
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
> >
> >
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> >
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--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Sep 02 2014 - 14:30:02 PDT
