[chimera-dev] hydrogen optimization

Terry Downing terry at francisco.compchem.ucsf.edu
Tue Aug 13 18:00:12 PDT 2002


  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

P. Therese Downing
Kuntz Lab

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