Hi Marek, You might also want to take a look at PROPKA, developed by the Jensen group, University of Copenhagen: <http://propka.ki.ku.dk/> 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. Best, 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 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