# Energy minimization file

**URL:** <https://gromacs.bioexcel.eu/t/energy-minimization-file/5340>\
**Category:** User discussions\
**Created:** [November 30, 2022, 8:10am UTC](https://gromacs.bioexcel.eu/t/energy-minimization-file/5340 "2022-11-30T08:10:43Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![Khadijah5780](https://avatars.discourse-cdn.com/v4/letter/k/ebca7d/32.png) [@Khadijah5780](https://gromacs.bioexcel.eu/u/Khadijah5780)\
**Post date:** [November 30, 2022, 8:10am UTC](https://gromacs.bioexcel.eu/t/energy-minimization-file/5340/1 "2022-11-30T08:10:43Z")

</div>

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](http://www.mdtutorials.com/gmx/complex/06_equil.html) by JUSTIN LEMKUL. Thank you.

---

<div class="post-metadata">

**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [November 30, 2022, 2:37pm UTC](https://gromacs.bioexcel.eu/t/energy-minimization-file/5340/2 "2022-11-30T14:37:21Z")

</div>

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.