[Chimera-users] protonating the protein

Elaine Meng meng at cgl.ucsf.edu
Mon Aug 11 10:19:23 PDT 2008

Hi Francesco,
> However, if you are using charges assigned in Chimera for something
> (Dock Prep with AddH, Add Charge,  and write Mol2 for input to DOCK
> scoring grid calculations, for example), you would need to add the
> protons in Chimera before assigning charges.  This could be done by
> selecting the carboxylate oxygens you want to get protonated (no more
> than one per carboxylate group, of course) and changing their atom
> types with the command:
>   setattr a idatmType O3 sel
> prior to running AddH and Add Charge (alone or as steps in Dock
> Prep).  It is not necessary to rename the residues.  Add Charge will
> then recognize the neutral forms of ASP and GLU and use the
> corresponding partial charges.  I just tested this in the Chimera
> production release, 1.2540 (July 9).

The above is definitely true, you do not need to rename the residues  
in Chimera, but further tests reveal to get the correct charge  
distribution on the protonated carboxylic acid, the atom names also  
need to match the AMBER lib files:  the protonated oxygen should be  
named OE2 (if glutamic acid) or OD2 (if aspartic acid) and the "free"  
oxygen should be named OE1/OD1.  This will already be true sometimes,  
but not always.  If you need to switch the atom names around before  
adding charges, it can be done by text-editing the PDB file or with  
commands.  For example, you could change the name of an atom by  
selecting it and then using a command like:
   setattr a name OE2 sel
After assigning charges, you can see the values as labels, for example:
   labelopt info charge
   la :6.a
Again all this was tested in the production release 1.2540.

Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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