[phenixbb] force field of PHENIX.refine ?

Nathaniel Echols nechols at lbl.gov
Thu Dec 2 15:48:32 PST 2010

On Thu, Dec 2, 2010 at 3:43 PM,  <chene at umbi.umd.edu> wrote:
> Dear authors of PHENIX,
> I just want to know what force field is used by phenix.refine,
> especially for simulated annealing, CHARMM, AMBER, or what else?

(Re-sending my reply to the list for anyone else who's interested...)

We're mostly using the CCP4 monomer library, which Refmac also uses.
The molecular dynamics in Phenix doesn't deal with electrostatics at
all, and thus isn't directly comparable to dedicated MD programs like
CHARMM or AMBER.  I think there are some other simplifications too
(like the lack of any solvent model).  It's not intended to be
physically accurate, since we're only interested in optimizing against
experimental data, and the X-ray term keeps the protein from exploding
in the absence of attractive forces.


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