# Error during EM

**URL:** <https://gromacs.bioexcel.eu/t/error-during-em/1198>\
**Category:** User discussions\
**Created:** [December 4, 2020, 10:44am UTC](https://gromacs.bioexcel.eu/t/error-during-em/1198 "2020-12-04T10:44:21Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![Sara](https://avatars.discourse-cdn.com/v4/letter/s/a5b964/32.png) [@Sara](https://gromacs.bioexcel.eu/u/Sara)\
**Post date:** [December 4, 2020, 10:44am UTC](https://gromacs.bioexcel.eu/t/error-during-em/1198/1 "2020-12-04T10:44:21Z")

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Hey everyone!  
I am running a simulation with a complexe of a protein and a ligand whose input files are prepared by CGennFF server.I have got this error in EM step:

 ![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/1X/345b56074e6b5efea8cb92d16a7eaef9e5a14c5d.png)

it stops in 15th step. As I surfed the internet, I found there might be a problem in ligand topology file. however, I don’t have any idea how to fix this.  
-SARA

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**Author:** ![cblau](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/cblau/32/5_2.png) [@cblau](https://gromacs.bioexcel.eu/u/cblau)\
**Post date:** [December 4, 2020, 11:51am UTC](https://gromacs.bioexcel.eu/t/error-during-em/1198/2 "2020-12-04T11:51:58Z")

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Hi,

This might be due to a few atoms being very close to one another - energy minimisation would attempt to move a few of them along an energy gradient, but in a scenario with lots of interactions end up placing them on top of another.

I suggest you have a look at atom 7932. Another option you could try is decreasing the initial step–size for the energy minimisation.

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**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:** [December 4, 2020, 2:11pm UTC](https://gromacs.bioexcel.eu/t/error-during-em/1198/3 "2020-12-04T14:11:46Z")

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Infinite energy usually means unrealistic coordinates. I doubt the problem is the topology itself but complete details of troubleshooting protein-ligand complexes are given at [http://manual.gromacs.org/current/user-guide/terminology.html#diagnosing-an-unstable-system](http://manual.gromacs.org/current/user-guide/terminology.html#diagnosing-an-unstable-system)

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<div class="post-metadata">

**Author:** ![Sara](https://avatars.discourse-cdn.com/v4/letter/s/a5b964/32.png) [@Sara](https://gromacs.bioexcel.eu/u/Sara)\
**Post date:** [February 23, 2021, 6:41am UTC](https://gromacs.bioexcel.eu/t/error-during-em/1198/4 "2021-02-23T06:41:01Z")

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thank you all.