[AMBER] Alanine scan of nonnatural amino acid

From: Aronica, Pietro <pietro.aronica07.imperial.ac.uk>
Date: Tue, 23 Aug 2016 09:21:37 +0000


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>
  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? Am I missing something? I'm pretty sure that the input files are all correct, mostly because they've been generated procedurally along with the ones for the other amino acid scans, which worked perfectly. I've also checked them to be extra sure and there should be no errors. MMPBSA.py works correctly when doing a "vanilla" gb or pb calculation of the interaction energy if the non natural residue is in the system. Is it just because of a nonstandard amino acid being involved in alanine scanning? If so, is there a workaround? If not, what else can I do to diagnose the error?


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Received on Tue Aug 23 2016 - 02:30:02 PDT
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