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 - 12:00:02 PDT
