Error with !Combinatorial usage with epik protonation states

I tried to specify a !Combinatorial tag to set up several protonation states in the epik: block in a variant of the old abl-imatinib-explicit example:

---
options:
  minimize: yes
  verbose: yes
  output_dir: .
  number_of_iterations: 100
  nsteps_per_iteration: 500
  temperature: 300*kelvin
  pressure: 1*atmosphere
  restraint_type: Boresch
  softcore_beta: 0.0
  timestep: 2.0*femtoseconds
  platform: OpenCL

molecules:
  Abl:
    filepath: input/2HYY-pdbfixer.pdb
  STI:
    filepath: input/STI02.mol2
    epik:
      select: !Combinatorial [0, 1, 2]
      ph: 7.4
      ph_tolerance: 0.7
      tautomerize: no
    openeye:
      quacpac: am1-bcc
    antechamber:
      charge_method: null

solvents:
  pme:
    nonbonded_method: PME
    nonbonded_cutoff: 9*angstroms
    clearance: 9*angstroms
    positive_ion: Na+
    negative_ion: Cl-

systems:
  Abl-STI:
    receptor: Abl
    ligand: STI
    solvent: pme
    leap:
      parameters: [leaprc.ff14SB, leaprc.gaff, frcmod.ionsjc_tip3p]

protocols:
  absolute-binding:
    complex:
      alchemical_path:
        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, 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, 1.000, 1.00, 1.000, 1.00, 1.00]
        lambda_electrostatics: [1.00, 1.00, 1.00, 1.00, 1.00, 0.95, 0.90, 0.85, 0.80, 0.75, 0.70, 0.65, 0.60, 0.55, 0.50, 0.45, 0.40, 0.35, 0.30, 0.25, 0.20, 0.15, 0.10, 0.05, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.000, 0.00, 0.000, 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, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 0.95, 0.90, 0.85, 0.80, 0.75, 0.70, 0.65, 0.60, 0.55, 0.50, 0.45, 0.40, 0.35, 0.30, 0.25, 0.20, 0.15, 0.10, 0.075, 0.05, 0.025, 0.01, 0.00]
    solvent:
      alchemical_path:
        lambda_electrostatics: [1.00, 0.95, 0.90, 0.85, 0.80, 0.75, 0.70, 0.65, 0.60, 0.55, 0.50, 0.45, 0.40, 0.35, 0.30, 0.25, 0.20, 0.15, 0.10, 0.05, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00, 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, 1.00, 1.00, 1.00, 1.00, 1.00, 1.00, 0.95, 0.90, 0.85, 0.80, 0.75, 0.70, 0.65, 0.60, 0.55, 0.50, 0.45, 0.40, 0.35, 0.30, 0.25, 0.20, 0.15, 0.10, 0.00]

experiments:
  system: Abl-STI
  protocol: absolute-binding

The resulting error was:

[chodera@mskcc-ln1 abl-imatinib]$ cat ~/abl-imatinib-explicit.o7782194
Warning: no access to tty (Bad file descriptor).
Thus no job control in this shell.
Running simulation via MPI...
2016-11-09 01:25:20,615: MPI enabled.
2016-11-09 01:25:20,642: Setting up the systems for Abl, STI_2 and pme
Invalid Range specified. Use '-h' option for usage
FATAL m2io_file_new(): Can't get first token from file: /cbio/jclab/home/chodera/github/choderalab/yank/yank-examples/examples/binding/abl-imatinib/setup/molecules/STI_2/STI_2-epik.mae. File is empty.
m2io_open failed for file /cbio/jclab/home/chodera/github/choderalab/yank/yank-examples/examples/binding/abl-imatinib/setup/molecules/STI_2/STI_2-epik.mae.
2016-11-09 01:25:37,341: ERROR - openmoltools.schrodinger - b'ERROR: ERROR: output from the converter is missing: /cbio/jclab/home/chodera/github/choderalab/yank/yank-examples/examples/binding/abl-imatinib/setup/molecules/STI_2/STI_2-epik.sdf\n'
2016-11-09 01:25:37,341: ERROR - openmoltools.schrodinger - Command '['/cbio/jclab/share/schrodinger/schrodinger2016-3/utilities/structconvert', '-imae', '/cbio/jclab/home/chodera/github/choderalab/yank/yank-examples/examples/binding/abl-imatinib/setup/molecules/STI_2/STI_2-epik.mae', '-osd', '/cbio/jclab/home/chodera/github/choderalab/yank/yank-examples/examples/binding/abl-imatinib/setup/molecules/STI_2/STI_2-epik.sdf']' returned non-zero exit status 1

Am I not allowed to specify a !Combinatorial option there, or does this have to appear in a specific order?

[jchodera]

OK, the issue is that epik only gives two protonation states for a pH tolerance of 0.7.

Interestingly, epik is run multiple times—once for each set combinatorial option. Since it’s so fast, this doesn’t impact performance. But we should probably increase the pH tolerance in our example documentation by a lot so people don’t run into this problem. It shouldn’t slow things down any.

[jchodera]

https://github.com/choderalab/yank/pull/555 fixed some lingering issues!