How to resolve the run_inflategro.sh error in Gromacs Membrane Protein Tutorial

User discussions
,
1

GROMACS version: 2021.4
GROMACS modification: No

I was trying the GROMACS Membrane Protein: KALP15 in DPPC tutorial.

Everything work smoothly until I reached the Step Three: Defining the Unit Cell & Adding Solvent.
Especially when I ran run_inflategro.sh.

It gave me the following error:

GROMACS:      gmx trjconv, version 2021.4
Executable:   /home/ubuntu/storage1/gromacs_gpu/bin/gmx
Data prefix:  /home/ubuntu/storage1/gromacs_gpu
Working dir:  /home/ubuntu/storage1/molecular_dynamics/gromacs_membrane_protein_tutorial
Command line:
  gmx trjconv -s system_shrink1_em.tpr -f system_shrink1_em.gro -o tmp.gro -pbc mol


-------------------------------------------------------
Program:     gmx trjconv, version 2021.4
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 275)
Function:    void gmx::CommandLineParser::parse(int*, char**)

Error in user input:
Invalid command-line options
  In command-line option -s
    File 'system_shrink1_em.tpr' does not exist or is not accessible.
    The file could not be opened.
      Reason: No such file or directory
      (call to fopen() returned error code 2)
  In command-line option -f
    File 'system_shrink1_em.gro' does not exist or is not accessible.
    The file could not be opened.
      Reason: No such file or directory
      (call to fopen() returned error code 2)

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
mv: cannot stat 'tmp.gro': No such file or directory
########################################
#
# RUNNING SHRINKING ITERATION 2...
#
########################################
system_shrink1_em.gro does not exist! Exiting.

Subsequently:

gmx solvate -cp system_shrink26_em.gro -cs spc216.gro -o system_solv.gro -p topol.top

didn’t work.

But this worked:

gmx solvate -cp system_shrink1.gro -cs spc216.gro -o system_solv.gro -p topol.top

Is using the latter command correct? If not, how can I resolve the problem?