olv52-FreeEnergyProtocol.txt

Name

alchemical free energy protocol with average network analysis using same charge compounds

Software

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

Parameter

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

olv52-PosePredictionProtocol.txt

Name

Maestro/ Released crystal structure

Software

Maestro 11 (Beta Version)

System Preparation Parameters

Assumed pH 7.4
Tautomers considered

System Preparation Method

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.