Hi Barb, There are two issues here. One was that though the heavy-atom positions were identical, the added hydrogens weren't positioned identically because of "steric clashes" between the two molecules when placing hydrogens (this was in some fairly newly-added code). I modified the new code to ignore clashes between sibling submodels (other analogous older code was already doing this). With the modified code and with the two PDB files merged so that the molecules open into model 0.1 and 0.2, the hydrogens get added identically. The other issue is that antechamber only determines charges to somewhere around 0.01 accuracy, even with the atoms at identical positions. Now, Chimera is supplying antechamber with identical positions, but giving them in a different order between the two residues, so that the resulting output isn't identical. I've modified the add-charge code so that it will now present the atoms in the same order as they were input -- so the result is that the charges vary only minimally now. Nonetheless, they shouldn't really be perceived as more accurate than about +/-0.01 charge units. You'd probably have to ask on the Amber mailing list why this is so and if there is anything that can be done or will be done about it. These changes will be available in tonight's daily build, which you could get tomorrow from www.cgl.ucsf.edu/chimera -- follow the "Daily Builds" link. --Eric On Sep 3, 2008, at 6:17 AM, Barb Truitt wrote:
Eric - Thank you for your help. I find the Chimera list incredibly helpful. I've verified that the pdb files have the same coordinates. I also redid the DOCK PREP without any rotation of either molecule and still have different charge assignments. Here are the four files. The carbons that vary the most between the two are the ones in the aromatic ring with a single methoxy group and the ones near the chlorine. I'm also sending an Excel file where I've sorted the atoms based on their coordinates so that I could check the assigned charges. I've color-coded the carbons that vary significantly.
Barb <charge comparison .xls
< SSR149415 .pdb><SSR149415_SR4.pdb><SSR149415_SR_T.mol2><SSR149415_T.mol2>