Energy minimization file

User discussions
1

GROMACS version:
GROMACS modification: Yes/No

Hi,

I am currently doing molecular dynamic simulation at the point to merge ligand and protein using this command:

gmx make_ndx -f em.gro -o index.ndx

Unfortunately, this error come out:

Error in user input:
Invalid command-line options
In command-line option -f
File ‘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)

I check my directory file and turn out em.gro file was absent. May I know how to create the em.gro file because I am following step from GROMACS TUTORIAL : Protein-Ligand Complex by JUSTIN LEMKUL. Thank you.

2

If there is no em.gro that means either you produced it in a different directory and need to be working there, or the mdrun process failed such that the final snapshot was not generated. Either way, the error simply means the file you’re trying to use doesn’t exist where you’re working.