[gmx-users] Unable to run gmx_mpi genion non-interactively

[Sarah Lucas]

Dear GMX experts,

I am trying to model a protein building its ligand but am having trouble generating the ions before I proceed with the energy minimization.  I have been following the Protein-Ligand tutorial and able to make the commands run non-interactively using MPI.  I tried following http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts to no avail. Currently, I am using Gromacs/2016.4.d with intel/2018.5.274 and impi same version. I tried using Gromacs/2019.1. My other option is version 5.0.4 Does anyone have a suggestion how to run genion non-interactively? Below are the line from my slurm file and the outputs it generated.

SLURM file command:
mpirun -np $MPI_NTASKS gmx_mpi_d genion -s wt_model_ions.tpr -o wt_model_solv.ions.gro -p topol_model.top -nname CL -nn 3 < sol.txt

sol.txt contains
15

Error File:
Fatal error:
Group     0 (         System) has 105532 elements
Group     1 (        Protein) has  6216 elements
Group     2 (      Protein-H) has  3110 elements
Group     3 (        C-alpha) has   399 elements
Group     4 (       Backbone) has  1197 elements
Group     5 (      MainChain) has  1595 elements
Group     6 (   MainChain+Cb) has  1963 elements
Group     7 (    MainChain+H) has  1966 elements
Group     8 (      SideChain) has  4250 elements
Group     9 (    SideChain-H) has  1515 elements
Group    10 (    Prot-Masses) has  6216 elements
Group    11 (    non-Protein) has 99316 elements
Group    12 (          Other) has    49 elements
Group    13 (            LIG) has    49 elements
Group    14 (          Water) has 99267 elements
Group    15 (            SOL) has 99267 elements
Group    16 (      non-Water) has  6265 elements
Select a group:
-------------------------------------------------------
Program:     gmx genion, version 2016.4
Source file: src/gromacs/topology/index.cpp (line 930)
MPI rank:    3 (out of 16)
Fatal error:
Cannot read from input

Output File:
Will try to add 0 NA ions and 3 CL ions.
Select a continuous group of solvent molecules

Thank you very much for your assistance,
Sarah