Re: [AMBER] protein-peptide alanine scaning

From: Jason Swails <>
Date: Tue, 02 Sep 2014 15:03:15 -0400

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 using the command bellow:
> -O -i -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).


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Tue Sep 02 2014 - 12:00:02 PDT
Custom Search