[Chimera-users] Dielectric ; Steepest descent

r charbel maroun rmaroun at gmail.com
Wed Sep 29 08:55:34 PDT 2010

Hi everybody,

The value of the dielectric constant used by Chimera is 1, corresponding to
calculations in vacuo. Is there not an easy way to change this value to, say
78 or to include a sigmoid function or the Generalized Born approach so as
to mime the presence of the solvent ? I looked for it but couldn't find it :
where in the {chimera_install_location}/share/MMMD/MMTKinter.py file can the
value of the dielectric be changed ? Otherwise, how to mime implicitly the
solvent ?

Also, it seems that only the Steepest descent, and not the Conjugate
gradients method, for energy minimization has been implemented in Chimera.
Why is this so?

It'd be so nice to have these two functionalities added as I don't know of
any free academic program allowing us to do energy minimization with these
options without having to parametrize every new ligand (Charmm, Namd), a
painful task.


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