[AMBER] protein-peptide alanine scaning

From: Renato Freitas <renatoffs.gmail.com>
Date: Tue, 2 Sep 2014 13:12:21 -0400

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_
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.


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Received on Tue Sep 02 2014 - 10:30:02 PDT
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