[Chimera-users] Protonation of selected atoms ?

Elaine Meng meng at cgl.ucsf.edu
Thu Nov 28 07:32:50 PST 2013

Hi Marek,
You might also want to take a look at PROPKA, developed by the Jensen group, University of Copenhagen:

Although developed originally for proteins, it looks like it has been extended to "ligands" as well.  I haven't tried it on nonproteins, but there are some literature references on that page that discuss the method and how it has been extended.
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Nov 28, 2013, at 5:44 AM, Marek Maly wrote:

> Dear Eric and Elaine,
> thank you very much for your help !
> My request comes from the fact that depending e.g. on pH
> in general just the certain percentage of protonable groups
> is really protonated. This for sure holds for "synthetic" polymers
> but perhaps also for proteins.
> To adjust protonation states on proteins I am using H++ server
> ( http://biophysics.cs.vt.edu/ ) which is the specialized/sofisticated
> software e.g. to calculate ionic state of the protonable groups taking here
> in account pH, dielectric constants (internal/external), micro-environment
> of the protonable groups etc. Unfortunately this tool seems to works "just" for the proteins
> (not for example for synthetic polymers or other molecules).
> So I appreciated the possibility to add hydrogens to the molecular structure in Chimera.
> Both advices (Elain's and Eric's) might be used to achieve desired partial protonation
> of the molecular structure using actual chimera possibilities however depending on the size of the structure and depending on the percentage of the protonation and depending on the eventual additional requirements regrading  distribution of the protons between different molecular residues
> (e.g. those containing primary amines, those containing secondary amines those containing tertiary
> amines ...) it might be still more or less "dirty" manual work.
> So if may I suggest something for the future Chimera development, it would be perhaps the possibility
> to protonate just the given percentage (e.g. with random distribution) of certain kind of protonable atoms (e.g. primary, secondary, tertiary amines , O atoms on COO groups ) which moreover belongs just to actually selected molecular part. Of course that regarding "steric clashes" etc. also the "non-selected" parts of the structure should be always considered in the process of protonation of the actually selected parts.
>   Best wishes,
>            Marek

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