On Tue, Aug 23, 2016 at 5:21 AM, Aronica, Pietro <
pietro.aronica07.imperial.ac.uk> wrote:
> Hello,
>
> I am running an alanine scan along a peptide using the appropriate module
> in MMPBSA.py. For the other eight positions, the protocol has worked fine,
> giving good results (which also correlate with experiment, but I
> digress...). However, in a position occupied by a non natural amino acid,
> the protocol fails, and gives the following error:
>
>
> Loading and checking parameter files for compatibility...
> mmpbsa_py_energy found! Using /usr/local/amber14/bin/mmpbsa_py_energy
> cpptraj found! Using /usr/local/amber14/bin/cpptraj
> Preparing trajectories for simulation...
> Mutating trajectories...
> File "/usr/local/amber14/bin/MMPBSA.py", line 103, in <module>
> app.file_setup()
> File "/usr/local/amber14/lib/python2.7/site-packages/MMPBSA_mods/main.py",
> line 169, in file_setup
> self.normal_system, self.mutant_system, self.pre)
> File "/usr/local/amber14/lib/python2.7/site-packages/MMPBSA_mods/make_trajs.py",
> line 328, in make_mutant_trajectories
> com_mut.MutateTraj(pre + 'mutant_complex.%s.%d' % (trj_suffix, rank))
> File "/usr/local/amber14/lib/python2.7/site-packages/MMPBSA_mods/alamdcrd.py",
> line 284, in MutateTraj
> new_coords = self._mutate(orig_resname, coords_tomutate)
> File "/usr/local/amber14/lib/python2.7/site-packages/MMPBSA_mods/alamdcrd.py",
> line 346, in _mutate
> if _getnumatms(resname) * 3 == len(coords):
> File "/usr/local/amber14/lib/python2.7/site-packages/MMPBSA_mods/alamdcrd.py",
> line 110, in _getnumatms
> 'in alamdcrd.py and reinstall MMPBSA.py' % resname))
> TypeError: not all arguments converted during string formatting
> Exiting. All files have been retained.
>
>
> Is this a known issue? Does the alanine scanning function of MMPBSA.py not
> work with non natural residues?
​Support is hard-coded for all of the natural amino acids. You will have
to add support for your non-natural amino acid by hand -- have a look at
alamdcrd.py for that.
HTH,
Jason
--
Jason M. Swails
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Received on Tue Aug 23 2016 - 09:30:02 PDT
