alchemical free energy protocol with average network analysis using same charge compounds
FESetup release 1.3dev, SUI version: 0.8.1, somd-freenrg 2016.1.1, pymbar version 3.0.0.dev0.dev-Unknown, Networkx v.1.11, networkanalysis v 0.1.1+23.ge21fdef
forcefield amber, ff14sb, tip3p, hfe
gaff2
mdengine, amber pmemd
AFE.type sire
AFE.separate_vdw_elec false
box.type = rectangular
box.length = 12.0
neutralize = False
temperature = 300 K
pressure = 1 atm
nmoves = 20000
ncycles = 100
buffered coordinates frequency = 5000
save coordinates = True
timestep = 2 * femtosecond
constraint = hbonds-notperturbed
hydrogen mass repartitioning factor = 1.0
cutoff type = cutoffperiodic
cutoff distance = 10*angstrom
barostat = True
andersen = True
energy frequency = 250
precision = mixed
minimise = True
equilibrate = False
equilibration iterations = 5000
center solute = True
reaction field dielectric = 82.0
minimal coordinate saving = True
lambda array varying between 9-27 evenly spaced lambda windows
Maestro/ Released crystal structure
Maestro 11 (Beta Version)
Assumed pH 7.4
Tautomers considered
Released structure 1ymrc was used as initial structure to build the receptor. The missing fragment Y264 - K279 was modelled from the FXR-FXR_17 complex structure 1hqmf released by the organisers. Sidechains within 4 Angstrom of FXR17 were rearranged in the final receptor structure to resemble 1hqmf orientation.