Hi!

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.pdb

Start residue of secondary structure  not found: HELIX    1   1 LEU      2  LEU     10  1                                   8

Model 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 3

Use 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.