message: Thanks to Adrian Roitberg for the tip about single-point antechamber
diff: @@ -25,7 +25,9 @@ def getMetaData():
  metaData["description"] = "Calculate atomic partial charges using AM1-BCC"
  metaData["charges"] = True
  metaData["potential"] = False
  - metaData["elements"] = "1,6,7,8,9,14,15,16,17,35,53" # H, C, N, O, F, Si, S, P, Cl, Br, I
  + metaData[
  + "elements"
  + ] = "1,6,7,8,9,14,15,16,17,35,53" # H, C, N, O, F, Si, S, P, Cl, Br, I
  return metaData
  @@ -50,12 +52,48 @@ def charges():
  lig1 = tempdir + "/" + "lig1.mol2"
  lig2 = tempdir + "/" + "lig2.mol2"
  output = subprocess.run(
  - [binary, '-i', name, '-fi', 'sdf', '-o', lig1, '-fo', 'mol2', '-c', 'bcc'],
  - stdout=subprocess.PIPE, cwd=tempdir, check=True
  + [
  + binary,
  + "-i",
  + name,
  + "-fi",
  + "sdf",
  + "-o",
  + lig1,
  + "-fo",
  + "mol2",
  + "-c",
  + "bcc",
  + "-pf",
  + "y",
  + "-ek",
  + "maxcyc=0, qm_theory='AM1', scfconv=1.d-10, ndiis_attempts=700,"
  + ],
  + stdout=subprocess.PIPE,
  + cwd=tempdir,
  + check=True,
  )
  output = subprocess.run(
  - [binary, '-i', lig1, '-fi', 'mol2', '-o', lig2, '-fo', 'mol2', '-c', 'wc', '-cf', 'charges'],
  - stdout=subprocess.PIPE, cwd=tempdir, check=True
  + [
  + binary,
  + "-i",
  + lig1,
  + "-fi",
  + "mol2",
  + "-o",
  + lig2,
  + "-fo",
  + "mol2",
  + "-c",
  + "wc",
  + "-cf",
  + "charges",
  + "-pf",
  + "y",
  + ],
  + stdout=subprocess.PIPE,
  + cwd=tempdir,
  + check=True,
  )
  # instead we read the "charges.txt" file
  result = ""
  