Trouble parsing `gro` and `top` files

I’m trying to run a YANK calculation using gromacs system inputs. Following the example here, my yaml script includes the following entries:

systems:
  gromacs-system:
    phase1_path: [HV149/System/topol.top, HV149/System/6md_mol.gro]
    phase2_path: [HV149/ligand/lig.top, HV149/ligand/ions.gro]
    ligand_dsl: resname V49
    solvent_dsl: resname SOL 
    gromacs_include_dir: /cbio/jclab/home/rossg/gromacs/share/top/amber99sb-ildn.ff/ 

However, there seems to be a problem with the file types as I get the following error message when I run yank:

Wrong system file types provided.
Extensions provided: ['gro', 'top']
Expected extensions: ['inpcrd', 'prmtop']

Wrong system file types provided.
Extensions provided: ['gro', 'top']
Expected extensions: ['inpcrd', 'prmtop']

Correctly recognized files ['HV149/System/topol.top', 'HV149/System/6md_mol.gro'] as ['gro', 'top']
Correctly recognized files ['HV149/ligand/lig.top', 'HV149/ligand/ions.gro'] as ['gro', 'top']
Correctly recognized files ['HV149/System/topol.top', 'HV149/System/6md_mol.gro'] as ['gro', 'top']
Correctly recognized files ['HV149/ligand/lig.top', 'HV149/ligand/ions.gro'] as ['gro', 'top']
Correctly recognized files ['HV149/System/topol.top', 'HV149/System/6md_mol.gro'] as ['gro', 'top']
Correctly recognized files ['HV149/ligand/lig.top', 'HV149/ligand/ions.gro'] as ['gro', 'top']
Wrong system file types provided.
Extensions provided: ['gro', 'top']
Expected extensions: ['pdb', 'xml']

2017-05-04 11:45:20,121: ERROR - yank.yamlbuild - System gromacs-system: _system_files(['HV149/System/topol.top', 'HV149/System/6md_mol.gro']) raised RuntimeError("Wrong system file types provided.\nExtensions provided: ['gro', 'top']\nExpected extensions: ['pdb', 'xml']\n",)
Traceback (most recent call last):
  File "/cbio/jclab/home/rossg/miniconda2/bin/yank", line 11, in <module>
    load_entry_point('yank==0.15.2', 'console_scripts', 'yank')()
  File "/cbio/jclab/home/rossg/miniconda2/lib/python2.7/site-packages/yank/cli.py", line 71, in main
    dispatched = getattr(commands, command).dispatch(command_args)
  File "/cbio/jclab/home/rossg/miniconda2/lib/python2.7/site-packages/yank/commands/script.py", line 97, in dispatch
    yaml_builder = YamlBuilder(yaml_source=yaml_path)
  File "/cbio/jclab/home/rossg/miniconda2/lib/python2.7/site-packages/yank/yamlbuild.py", line 1221, in __init__
    self.parse(yaml_source)
  File "/cbio/jclab/home/rossg/miniconda2/lib/python2.7/site-packages/yank/yamlbuild.py", line 1314, in parse
    self._db.systems = self._validate_systems(yaml_content.get('systems', {}))
  File "/cbio/jclab/home/rossg/miniconda2/lib/python2.7/site-packages/yank/yamlbuild.py", line 1861, in _validate_systems
    raise YamlParseError('System {}: {}'.format(system_id, e.autos[-1]))
yank.yamlbuild.YamlParseError: System gromacs-system: _system_files(['HV149/System/topol.top', 'HV149/System/6md_mol.gro']) raised RuntimeError("Wrong system file types provided.\nExtensions provided: ['gro', 'top']\nExpected extensions: ['pdb', 'xml']\n",)

Are gromacs files not yet supported?

[gregoryross]

Thanks @andrrizzi! Adding solvents key removed that error. I’ll close this issue.

[andrrizzi]

Also, notice that if you specify solvent_dsl: resname SOL you need to have counterions named SOL too or yank won’t treat them as solvent counterions. SOL is among the names automatically recognized by Yank so you can remove the solvent_dsl altogether. Alternatively you’ll need to add manually the DSL of your counterions.