[Chimera-users] Acylation of peptide

Remmer Salas remmersalas at yahoo.com
Thu May 7 09:23:25 PDT 2015

I am new to Chimera and I am trying to modify the PDB file of a peptide by acylation. I have also a PDB file for the fatty acid which I got by removing the bound protein. I used the join models to form a peptide bond but prompted with this error:

 The following problems occurred while reading PDB file for anomt1.pdbStart residue of secondary structure  not found: HELIX    1   1 LEU      2  LEU     10  1                                   8Model 1 (anomt1.pdb) appears to be a protein without secondary structure assignments.Automatically computing assignments using 'ksdssp' and parameter values:  energy cutoff -0.5  minimum helix length 3  minimum strand length 3Use command 'help ksdssp' for more information.TypeError Exception in Tk callback  Function: <bound method BuildStructureDialog._addParamBond of <BuildStructure.gui.BuildStructureDialog object at 0x04F9FBF0>> (type: <type 'instancemethod'>)  Args: ()Traceback (innermost last):  File "C:\Program Files\Chimera 1.10.1\bin\lib\site-packages\Pmw\Pmw_1_3_3\lib\PmwBase.py", line 1747, in __call__    return apply(self.func, args)  File "C:\Program Files\Chimera 1.10.1\share\BuildStructure\gui.py", line 313, in _addParamBond    self._appbDihedral.get(), phi=self._appbPhi.get())  File "C:\Program Files\Chimera 1.10.1\share\BuildStructure\__init__.py", line 869, in cnPeptideBond    cn[1].residue.phi = phi  File "C:\Program Files\Chimera 1.10.1\share\chimera\phipsi.py", line 91, in setPhi    _setAngle(bond, phi, getPhi(res), "phi")  File "C:\Program Files\Chimera 1.10.1\share\chimera\phipsi.py", line 134, in _setAngle    br.angle = (newAngle - curAngle, br.biggerSide())TypeError: unsupported operand type(s) for -: 'float' and 'NoneType'
TypeError: unsupported operand type(s) for -: 'float' and 'NoneType'
  File "C:\Program Files\Chimera 1.10.1\share\chimera\phipsi.py", line 134, in _setAngle    br.angle = (newAngle - curAngle, br.biggerSide())

My first question is how to solve this error. Second, how can I optimize the generated PDB file using Chimera? I want also to convert this optimize PDB file to PQR.
Any advice is greatly appreciated.
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