[Chimera-users] Protonating the protein

Francesco Pietra chiendarret at gmail.com
Thu Aug 7 03:38:30 PDT 2008

I am not saying anything new. I have a (for me) difficult problem of
protonating a protein homology model (built with Modeller) where there
are several halogen ion ligands. Actually I succeeded in getting a
workable model. Chimera loads it and add hydrogens. I could even
prepare the model for DOCK6, generating spheres.

Now, however (and also because, before docking small ligands with
DOCK6, I want to dock polypeptides, probably with DOT2) I would like
to assign specific protonation states to certain carboxylic acids.
That is, I want to create an overall model where certain facing
carboxylic acids actually face as "carboxylate-carboxylic acid" or as
"carboxylic acid-carboxylic acid", or, finally, as
"carboxylate-carboxylate", the latter also with metal ligand in
between or not.

Question: to which extent can Chimera aid the task? And which other
package (pdb2qr, H++, ...) may aid Chimera? Or no other package, but
simply renaming the said residues in the pdb file and let Amber 10
(which is the package I'll use for MD, with ff99B ff for the protein)
do the job of eliminating clashes?

All that shows that I have no experience in selective protonation, and
the halide ions (in the above said work, I have them simply under
"ATOM" under the specific chain of the amino acid residues, not
"HETATM", as the latter caused a lot or problems) create difficulty to
protonating packages.

Thanks for giving me a general guideline along with best moving.

francesco pietra

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