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?
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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Received on Tue Sep 02 2014 - 13:00:02 PDT
