[Chimera-users] Acylation of peptide

Elaine Meng meng at cgl.ucsf.edu
Fri May 8 14:49:32 PDT 2015

Hi Remmer,
Note that the PDB2PQR server will omit any atoms for which the chosen force field does not have parameters.  You should look carefully at your output pqr file to see if it contains the fatty acid.  I don’t know which choices of force field in the PDB2PQR dialog, if any, will include the fatty acid.

On May 8, 2015, at 1:43 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Remmer,
> Based on your description, it sounds like the problem is choosing the “peptide bond” option when you are not actually forming a peptide bond between two amino acids.  (It should give a better error message instead of a traceback, of course!)
> Instead you would have to choose “other bond” and fill in the needed parameters.
> For optimization, see Minimize Structure (in menu under Tools… Structure Editing).  You may want to only minimize the region you have changed, see “fixed atoms” in that dialog. There is also a PDB2PQR tool (in menu under Tools… Structure Editing) that uses a web service to create a PQR file.
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/apbs/pdb2pqr.html>
> You can search for terms of interest such as “PQR” with Help… Search Documentation in the Chimera menu.
> I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D. 
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>> On May 7, 2015, at 9:23 AM, Remmer Salas <remmersalas at yahoo.com> wrote:
>> 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.
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