Dear Amber,
Thank you very much for your quickly answer.
I need to explain my doubt better...
If I do not have an amino acid side chain, Leap add all the missing side
chain atoms according to ONE conformation, (the conformation presented in
amber template).
My question is: Why amber developers chose to put in the template this ONE
conformation (and not other conformation from many possible conformations)?
(Is it the most populated conformation based on all the PDB structures
available? or ....?)
Thanks again!
Marta
2013/3/19 David A Case <case.biomaps.rutgers.edu>
> 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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--
Cumprimentos/ Best Regards/ Mit freundlichen Grüßen
Marta Andreia da Silva Perez Gomes
Post Doctoral Researcher
Laboratory of Computational Chemistry and Biochemistry
Ecole Polytechnique Fédérale de Lausanne, EPFL
<http://search.epfl.ch/ubrowse.action;jsessionid=C10659E229EB216209BCB30883F7B549?acro=EPFL>
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Received on Tue Mar 19 2013 - 06:00:03 PDT
