adding dummy atom
Posted: Thu Jun 29, 2017 3:51 pm
Greetings,
I want to add a CustomCentroidBondForce between the COM of the ligand and it's initial COM coordinates x0,y0,z0. For this purpose I thought to add a dummy atom to the system with mass=0. However, I still can't find how to set it's coordinates to x0,y0,z0. This is how my code looks like:
And then..? How do I set the coordinates? There is another function named parm.add_atom, but it is relevant to AmberParm. Which is the right way to do it?
I want to add a CustomCentroidBondForce between the COM of the ligand and it's initial COM coordinates x0,y0,z0. For this purpose I thought to add a dummy atom to the system with mass=0. However, I still can't find how to set it's coordinates to x0,y0,z0. This is how my code looks like:
Code: Select all
# Load the Amber files
parm = AmberParm(args.PRMTOP, args.COORD)
# Create the OpenMM system
# Load the Amber topology file
system = parm.createSystem(nonbondedMethod=CutoffNonPeriodic,
nonbondedCutoff=args.NONBONDED_CUTOFF*u.angstrom,
constraints=app.HBonds, rigidWater=True,
implicitSolvent=igb,
# implicitSolventKappa=0.107317448721*(1.0/u.angstrom), # the value for 0.2 M salt
implicitSolventSaltConc=args.SALTCON*u.moles/u.liter,
soluteDielectric=1.0,
solventDielectric=78.5,
removeCMMotion=True,
ewaldErrorTolerance=5e-05,
flexibleConstraints=False,
verbose=args.VERBOSE,
useSASA=False
COM_index = system.addParticle(0.0)