Hi Nihshanka, I'll try to answer your questions in a brief manner, but see the AddH man page for a full description: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/addh/addh.html AddH does not use a force field. It uses the atom types and rules to place hydrogens. For example, if there is an sp3-hybridized carbon, it knows there should be four bonds from that carbon in tetrahedral arrangement. If two things are already bonded to that carbon, two hydrogens will be added to complete the known valence. For some atoms, this completely determines the position of the hydrogens. For other atoms, such as a hydroxyl group, there is a degree of freedom, and additional information is used to place the hydrogen. The choices are "steric only" and "also consider H-bonds" - the first places the H to avoid clashes and the second places the H to both avoid clashes and form H-bonds where possible. AddH does not put charges on the structure. You could do that with Add Charge (or Dock Prep, which calls Add Charge). HOWEVER, DelPhi completely ignores the radii and charges that Chimera knows about. DelPhi uses only the radii and charges in the parameter files that you specify in DelPhiController. Depending on which parameter files you use in DelPhi, it might not even be necessary to add hydrogens. If an amino acid is forming different bonds, it will be protonated differently. If a residue is on the N-terminus of a chain, the most likely protonation state (and the one chosen by AddH) is -NH3(+). If a residue is on the C-terminus, the backbone ends in a carboxylate with the most likely protonation state -CO2(-). Force fields, or at least Amber, have different sets of charges for the same residue depending whether it is on the N-terminus, C-terminus, or in the middle of the chain. If the PDB file says that a cysteine is disulfide-bonded to another cysteine (sidechains forming an S-S bond), then no hydrogens are put on those sulfurs because they are already forming all the bonds they can. Histidine is a little different - the sidechain can be positively charged or neutral depending on its environment. You can have the program decide, or control it yourself by changing the residue name as described in the man page. In all these cases the force field will have different sets of charges for the different bonding patterns, usually indicated by different residue names, that add up to the appropriate formal charges. What these residue names should be depends on the specific force field or DelPhi parameter file. I hope this helps, Elaine On Aug 14, 2006, at 8:38 PM, Nihshanka Debroy wrote:
Hi, I have a couple of questions about the addH utility built into Chimera, and about PDB files in general. I used addH to protonate (add hydrogens) to PDB files. Does it use a force field of some kind in the process, like Amber or Charmm? It seems that depending on the force field used to protonate a PDB, the values for the partial charges and the van der waals radii are different. Specifically, I am using these charges and radii in the DelphiController. Another thing I've noticed is that when adding hydrogens, for the same amino acid, the hydrogens are sometimes different in name or number. For example if I have a Cysteine, in some cases, an HG (gamma hydrogen) is added for the gamma sulphur, balancing out charges completely. In other cases, the HG is not added, and so the amino acid ends up with a net negative charge. I was just wondering if this is supposed to happen. Here's another example. For Alanine, I was getting 1H, 2H and 3H attached to the nitrogen in some cases. In other cases, I just got "H" attached to the nitrogen. Does this mean those particular instances of ALA in the PDB had one only hydrogen attached to the nitrogen, instead of 3 ? Wouldn't the missing 2 hydrogens lead to a net negative charge on the ALA? Thanks for all the help and for this mailing list. It is a wonderful resource.
Sincerely, Nihshanka Debroy _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html