Greetings,
I am using the Parmed API to prepare a system for simulation with OpenMM. I
want to add a restraint 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 (or a
virtual site maybe?) to the system with mass=0 and fixed position. However,
I still couldn't find how to set the dummy atom's coordinates to x0,y0,z0.
This is how my code looks like:
from parmed.amber import AmberParm
# 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)
And then..? How do I set the coordinates? There is also the function
parm.add_atom which seemingly does the same thing. Which is the right way
to do it?
I thank you in advance (Jason Swails :D).
Thomas
--
======================================================================
Dr Thomas Evangelidis
Post-doctoral Researcher
CEITEC - Central European Institute of Technology
Masaryk University
Kamenice 5/A35/2S049,
62500 Brno, Czech Republic
email: tevang.pharm.uoa.gr
tevang3.gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Thu Jun 29 2017 - 16:30:03 PDT
