Amber

Amber is a widely used biomolecular simulation package for decades. Much of the simulation workflows are routine that can be automated and rendered on demand.

Input files

from atomea.schemas.workflow.amber import Amber22Inputs

amber_inputs = Amber22Inputs()
amber_inputs.imin = 1
amber_inputs.ntx = 1
amber_inputs.irest = 0
amber_inputs.ntmin = 1
amber_inputs.maxcyc = 5000
amber_inputs.ncyc = 1000
amber_inputs.ntr = 1
amber_inputs.restraint_wt = 2.0
amber_inputs.restraintmask = "!(:WAT) & (@C,CA,N,O,O5',P,O3',C3',C4',C5')"
amber_inputs.ntb = 1
amber_inputs.ntf = 1
amber_inputs.ntc = 1
amber_inputs.cut = 10.0
amber_inputs.ntxo = 2
amber_inputs.ntwr = 200
amber_inputs.ntpr = 1
amber_inputs.ntwx = 200
amber_inputs.ioutfm = 1
amber_inputs.iwrap = 1

amber_inputs.write_render("min.in")

&cntrl
    imin=1,
    irest=0,
    ntx=1,
    ntmin=1,
    maxcyc=5000,
    ncyc=1000,
    ig=-1,

    ...

    baroscalingdir=0,
    csurften=0,
    gamma_ten=0.0,
    ninterface=2,
    tol=1e-05,
    jfastw=0,
&end

Command

from atomea.schemas.workflow.amber import Amber22CLI

amber_cli = Amber22CLI(
    mdin="min.in",
    mdout="min.mdout",
    mdinfo="min.mdinfo",
    prmtop="mol.prmtop",
    inpcrd="mol.inpcrd",
)
amber_cli.module = "pmemd.cuda"
amber_command = amber_cli.render()

print(amber_command)

["pmemd.cuda -i min.in -o min.mdout -inf min.mdinfo -p mol.prmtop -c mol.inpcrd"]