Hi, I am attempting to add hydrogens to proteins with ligands bound...I am using the AddH extension, which appears to add hydrogens with reasonable bond lengths and bond angles...However, I notice that because default torsion angles are being used, there are situations in which the cartesian coordinates of the hydrogens are not optimized and result in clashes...This is particularly a problem with hydrogens that are attached to heavy atoms that are free to rotate (ie methyl and amide groups)...Are there any torsion minimization protocols available where I can optimize the torsional angle of just the newly added hydrogens without changing the cartesian coordinates of the heavy atoms (allow them to rotate to optimize the hydrogen placement but not move away from the experimental coordinates)?...I just spoke with Tom Ferrin and he said that Eric was the person most experienced with the AddH extension, and he recommended that I look at the documentation from both him and Elaine...Anything you can recommend on this would be greatly appreciated... Sincerely, P. Therese Downing Kuntz Lab