Issue with Ligand Coordinates During Absolute-Binding Free Energy

[davidcooper7]

As you can see in this image the ligand has basically exploded outside of the binding pocket or this transmembrane protein in which it is supposed to be. This image is from a .dcd that was extracted from the 0th state of the simulation of the netcdf complex file using the YANK method yank.analyze.extract_trajectory(). There are not the same issues with the input AMBER files. YANK doesn't have any issue running, or any noticeable warnings in the log file. I've tried many different options and such and got the same results. Any help would be great.

yaml:

---

experiments:
protocol: absolute-binding
restraint:
type: FlatBottom
restrained_receptor_atoms: resid 328 or resid 116 or resid 299 or resid 150
restrained_ligand_atoms: all
spring_constant: 10.0kilocalories_per_mole/(angstrom**2)
well_radius: 12.0angstroms
system: rec-lig
options:
default_nsteps_per_iteration: 1000
default_number_of_iterations: 1
default_timestep: 1.0femtosecond
minimize: no
number_of_equilibration_iterations: 0
output_dir: /media/volume/sdb/yank/morphine/morphine_test
platform: fastest
pressure: 1.0atmosphere
resume_simulation: yes
temperature: 300kelvin
verbose: yes
protocols:
absolute-binding:
complex:
alchemical_path:
lambda_electrostatics: [1.00, 1.00, 1.00, 1.00, 1.00, 0.90, 0.80, 0.70, 0.60, 0.50, 0.40, 0.30, 0.20, 0.10, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00]
lambda_sterics: [1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 0.90, 0.80, 0.70, 0.60, 0.50, 0.40, 0.30, 0.20, 0.10, 0.00]
lambda_restraints: [0.00, 0.25, 0.50, 0.75, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00]
solvent:
alchemical_path:
lambda_electrostatics: [1.00, 0.90, 0.80, 0.70, 0.60, 0.50, 0.40, 0.30, 0.20, 0.10, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00]
lambda_sterics: [1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 0.90, 0.80, 0.70, 0.60, 0.50, 0.40, 0.30, 0.20, 0.10, 0.00]
solvents:
PME:
nonbonded_cutoff: 8.0angstroms
nonbonded_method: PME
systems:
rec-lig:
ligand_dsl:resname UNL
phase1_path:
- /media/volume/sdb/yank/morphine/morphine_complex.inpcrd
-/media/volume/sdb/yank/morphine/morphine_complex.prmtop
phase2_path:
- /media/volume/sdb/yank/morphine/morphine_solvent.inpcrd
- /media/volume/sdb/yank/morphine/morphine_solvent.prmtop
solvent: PME