[Chimera-users] Re: [chimera-dev] add h

Elaine Meng meng at cgl.ucsf.edu
Wed Dec 8 10:13:17 PST 2004

On Dec 7, 2004, at 4:17 PM, Virginie Lafont wrote:
> I am a new user of chimera and I already have a question.
> I have an protonated aspartic acid in my protein and I was wondering,
> is it possible to add hydrogen atom to aspartic acid with chimera?
> Thanks
> Virginie

Hello Virginie,
It is possible, with a few steps.  As you already noticed,
if you just use "addh" the aspartic and glutamic acid carboxylate groups
will not get protonated.  In the definitions of these residues, the
carboxylate oxygen atoms are type O2-, which would not get protonated.

You can use Define Attribute to change the types of these atoms.
First you need to know the residue number of the aspartic acid you want
to protonate and which of the oxygens (OD1 or OD2) you want to receive
the proton.  Next, create a define attribute input file in which you  
these two atoms and change type of the oxygen you want protonated to O3
and the one you don't want protonated to type O2  (example attached).

  There is a file description and more examples in the manual page
  for Define Attribute,

In Chimera:
    open your PDB file of interest
    run addh        (note the aspartic acid is not protonated in this  
    Tools... Utilities... Define Attribute   (open the previously  
prepared input file)
    now run addh again      (note the aspartic acid will be protonated)

The proton may not be pointing the direction you want, so you will
probably then want to rotate the OH to the proper position, as  
described in

My define attribute example file (attached) works with the PDB file  
The define attribute file tells Chimera to change the atom types of   
Asp residue
number 7 in chain B so that the side chain will be neutralized when AddH
is run.

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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