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? Thanks. Chen Chen Chen, PhD, Research Associate Center for Advanced Research in Biotechnology (CARB), University of Maryland Biotechnology Institute (UMBI), 9600 Gudelsky Drive, Rockville, MD 20850 240-314-6122
Hi Chen, energy function: Grosse-Kunstleve RW, Afonine PV, Adams PD: cctbx news: Geometry restraints and other new features Newsletter of the IUCr Commission on Crystallographic Computing 2004, 4, 19-36. Target values: CCP4 Monomer Library and phenix.elbow or phenix.ready_set Pavel. On 12/2/10 3:43 PM, [email protected] 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? Thanks.
Chen
Chen Chen, PhD, Research Associate Center for Advanced Research in Biotechnology (CARB), University of Maryland Biotechnology Institute (UMBI), 9600 Gudelsky Drive, Rockville, MD 20850 240-314-6122
On Thu, Dec 2, 2010 at 3:43 PM,
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. -Nat
participants (3)
-
chene＠umbi.umd.edu -
Nathaniel Echols -
Pavel Afonine