On Tue, Mar 19, 2013, Marta Perez wrote:
> So, Leap adds the missing atoms in amino acids according to one
> conformation stored in the template.
> Why uses leap this conformation ? (Is it the most frequent rotamer ... ?
It is *very* arbitrary. You can generally use LEaP to place missing
hydrogens, since they will generally quickly optimize upon minimization
and dynamics. (Still, reduce is a better choice.) OXT is another atom
that LEaP generally adds acceptably.
LEaP is not a very good program to add other missing atoms, but again it
depends very much on the system and on what you plan to do with the structure
once you get it. Homology modeling programs are usually a better choice for
building model structures where most things are known, but a small number of
atoms (or residues) are missing.
....dac
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Received on Tue Mar 19 2013 - 05:30:03 PDT
