"No such group" during solvation step with octanol and charged solute

[rsexton2]

I'm trying to run

mdpow-equilibrium --solvent octanol glyh101.yml I did the same with --solvent water and had no issues.

I copied the runinput.yml from the templates and made a few changes (copied here as .txt). glyh101.txt

Here are the structure (step4.1_equilibration.gro) and topology (Glyh101.ipt) input files (copied here as .txt). Glyh101.txt step4.1_equilibration.txt

I got the following error

GROMACS:      gmx genion, version 2021.1
Executable:   /nfs/homes/rsexton/Library/miniconda3/envs/glyh101/bin/gmx
Data prefix:  /nfs/homes/rsexton/Library/miniconda3/envs/glyh101
Working dir:  /nfs/homes/rsexton/Projects/CFTR/glyh101/mdpow/glyh101/Equilibrium/octanol/solvation
Command line:
  gmx genion -nn 0 -o ionized.gro -p /nfs/homes/rsexton/Projects/CFTR/glyh101/mdpow/glyh101/Equilibrium/octanol/top/system.top -s topol.tpr -pname NA -np 1 -nname CL

Reading file topol.tpr, VERSION 2021.1 (single precision)
Reading file topol.tpr, VERSION 2021.1 (single precision)
Will try to add 1 NA ions and 0 CL ions.
Select a continuous group of solvent molecules
Group     0 (         System) has  7468 elements
Group     1 (          Other) has  7468 elements
Group     2 (            GYH) has    43 elements
Group     3 (           OcOH) has  7425 elements
Select a group: Error: No such group 'SOL'
Select a group: 
-------------------------------------------------------
Program:     gmx genion, version 2021.1
Source file: src/gromacs/topology/index.cpp (line 902)

Fatal error:
Cannot read from input

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
Traceback (most recent call last):
  File "/nfs/homes/rsexton/Library/miniconda3/envs/mdpow/bin/mdpow-equilibrium", line 62, in <module>
    S = equilibrium_simulation(cfg, opts.solvent, dirname=opts.dirname)
  File "/nfs/homes/rsexton/Library/miniconda3/envs/mdpow/lib/python2.7/site-packages/mdpow/run.py", line 227, in equilibrium_simulation
    maxwarn=maxwarn)
  File "/nfs/homes/rsexton/Library/miniconda3/envs/mdpow/lib/python2.7/site-packages/mdpow/equil.py", line 394, in solvate
    params = self._setup_solvate(**kwargs)
  File "/nfs/homes/rsexton/Library/miniconda3/envs/mdpow/lib/python2.7/site-packages/mdpow/equil.py", line 348, in _setup_solvate
    return gromacs.setup.solvate(**kwargs)
  File "/nfs/homes/rsexton/Library/miniconda3/envs/mdpow/lib/python2.7/site-packages/gromacs/setup.py", line 626, in solvate
    **kwargs)
  File "/nfs/homes/rsexton/Library/miniconda3/envs/mdpow/lib/python2.7/site-packages/gromacs/setup.py", line 492, in solvate_ion
    input=solvent_name)
  File "/nfs/homes/rsexton/Library/miniconda3/envs/mdpow/lib/python2.7/site-packages/gromacs/core.py", line 398, in __call__
    return self.run(*args, **kwargs)
  File "/nfs/homes/rsexton/Library/miniconda3/envs/mdpow/lib/python2.7/site-packages/gromacs/core.py", line 178, in run
    results, p = self._run_command(*_args, **_kwargs)
  File "/nfs/homes/rsexton/Library/miniconda3/envs/mdpow/lib/python2.7/site-packages/gromacs/core.py", line 611, in _run_command
    self.check_failure(result, command_string=p.command_string)
  File "/nfs/homes/rsexton/Library/miniconda3/envs/mdpow/lib/python2.7/site-packages/gromacs/core.py", line 566, in check_failure
    raise GromacsError(rc, msg)
gromacs.exceptions.GromacsError: [Errno 1] Gromacs tool failed
Command invocation: printf "SOL\n" | gmx genion -nn 0 -o ionized.gro -p /nfs/homes/rsexton/Projects/CFTR/glyh101/mdpow/glyh101/Equilibrium/octanol/top/system.top -s topol.tpr -pname NA -np 1 -nname CL

[iorga]

@rsexton2

Please check with @VOD555 for allowed values, but I don't think that solvent_name should be "OcOH", I would say rather "octanol", or better nothing, in this latter case it will take the default value from the option "--solvent octanol".

Also your molecule seems to be charged, but for solvation free energies and partition coefficients calculations we use only neutral form of the compounds.

[VOD555]

@iorga The solvent_name is the molecule type defined in the itp file. Althought it's SOL in [ moleculetype ] but gromacs still uses the atomtype in [ atom ] which is OcOH. I checked the itp files for water, they are all defined as SOL.

For octanol, the molecule type should be changed to SOL as well.

I will do this after finishing the PR #150