[MMTK] Energy minimization of amidated peptide

Konrad Hinsen research at khinsen.fastmail.net
Fri Jan 4 16:07:55 UTC 2013

Sabine Reisser writes:

 > I'm trying to energy minimize a 14 residue helical peptide with the last 
 > residue being an amide group.


 > When I run this, I get the Error:
 > [...]
 >    File "/usr/lib64/python2.7/site-packages/MMTK/ChemicalObjects.py", 
 > line 59, in __getattr__
 >      return getattr(self.type, attr)
 > AttributeError: 'AtomType' object has no attribute 'amber_atom_type'
 > When I just remove the amide group from the pdb file, minimization runs 
 > fine. How can I tell MMTK what the NHE group is?

Just call it NME and it should work fine!

Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: research AT khinsen DOT fastmail DOT net

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