Hi Francesco, If you know which carboxylates you want to be protonated and are going to use AMBER anyway, the most straightforward approach may be to simply rename the residues with the appropriate AMBER names (ASH and GLH, I believe, for the -COOH forms) and let AMBER take care of it. Performing MD will move everything around from the positions chosen by some other program anyway. 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). When you switch from one program to another, there are often naming/ formatting issues. Chimera generates hydrogen names to match the newer PDB specifications, while others may use older PDB hydrogen names or their own naming system (e.g. AMBER). To get the protonated structure from Chimera into AMBER, you might have to rename all the hydrogen atoms and those special residues, or maybe just delete all the hydrogens, rename the residues, and have AMBER add hydrogens back for its own calculations. There are some Web servers that add hydrogens after predicting which carboxylates (if any) or other ionizable groups should be protonated. Again, there may be formatting and naming issues - some servers output PQR format, which is not quite PDB format. If you are not sure which carboxylates should be protonated, you could simply run these predictions to help decide which residues to rename for hydrogen addition by AMBER. Here are a few of the many Web servers that can add hydrogens to structures: MolProbity (can add hydrogens with Reduce): http://molprobity.biochem.duke.edu/ H++ http://biophysics.cs.vt.edu/H++/ PROPKA/PDB2PQR http://propka.ki.ku.dk/~drogers/ Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Aug 7, 2008, at 3:38 AM, Francesco Pietra wrote:

Hi: 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