Tool Set Documentation

Amber Parameters

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param"ff94"force field: ff94, ff96, ff86, ff98, ff99, ff02, ff02EP, gaff
sdsteps50number of minimization steps for steepest descent min.
minsteps300number of minimization steps for ABNR min.
minetol1E-2energy gradient tolerance for min.
minstepsz0.005initial min. step size
minoutfrq10minimization output frequency
gbundefuse GB potential: tc6, tc, obc, jsb, mgb
gbsa0include surface area term in GB potential
gbeps80external dielectric for GB
cutoff14cutoff for non-bonded interactions
cut1use cutoff
epsilon1.0dielectric constant
dielec'CDIE'dielectric: cdie, rdie
dynsteps100dynamics steps
dyntstep0.002dynamics step size
dyntemp300dynamics temperature
dynitempundefdynamics initial temperature
dynseedundefrandom number generator seed
dynoutfrq10minimization output frequency
restrain0restraints from restraint file
rex0flag for running replica exchange
lambdaundeflambda value for thermodynamic integration
saltconundefsalt concentration for use with GB
rexmodeundef1: temperature, 2: lambda
dyntautp1.0temperature coupling