# Fix error for file creation **URL:** \ **Category:** User discussions\ **Tags:** mdp-parameters\ **Created:** [July 2, 2024, 6:03am UTC](https://gromacs.bioexcel.eu/t/fix-error-for-file-creation/9553 "2024-07-02T06:03:47Z")\ **Posts on this page:** 10\ **Page:** 1
**Author:** ![m.m](https://avatars.discourse-cdn.com/v4/letter/m/958977/32.png) [@m.m](https://gromacs.bioexcel.eu/u/m.m)\ **Post date:** [July 2, 2024, 6:03am UTC](https://gromacs.bioexcel.eu/t/fix-error-for-file-creation/9553/1 "2024-07-02T06:03:47Z")
Hi Excuse me, how do I fix the following error? fatal error: number of coordinates in coordinate file (solve.gro, 15537) does not match topology (topol.top, 15612) ---
**Author:** ![obZehn](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/obzehn/32/2629_2.png) [@obZehn](https://gromacs.bioexcel.eu/u/obZehn)\ **Post date:** [July 2, 2024, 8:14am UTC](https://gromacs.bioexcel.eu/t/fix-error-for-file-creation/9553/2 "2024-07-02T08:14:59Z")
This means that you have mismatching structure file and topology file, that is you modified in some way the .gro file which now has 75 less atoms than the topology you are referring to for compilation. What was the last thing you did? Added ions? Added water? Did you modify the box in any way? Remember that if you change the box content you have to update the topology accordingly. ---
**Author:** ![asif2](https://avatars.discourse-cdn.com/v4/letter/a/3da27b/32.png) [@asif2](https://gromacs.bioexcel.eu/u/asif2)\ **Post date:** [July 2, 2024, 8:21am UTC](https://gromacs.bioexcel.eu/t/fix-error-for-file-creation/9553/3 "2024-07-02T08:21:18Z")
Please indicate what stage of MD preparation you are performing. My guess is that you’re encountering an error in the solvation part. It’s just a minor indentation error. You open the topol.top file and go to the bottom of the file, where the sol 6720 is placed adjacent to the lig 1. So just put that sol 6720 in the next line, and also check the spacing between sol and 6720 i hope this will rectify your error. :-) ---
**Author:** ![m.m](https://avatars.discourse-cdn.com/v4/letter/m/958977/32.png) [@m.m](https://gromacs.bioexcel.eu/u/m.m)\ **Post date:** [July 3, 2024, 9:11am UTC](https://gromacs.bioexcel.eu/t/fix-error-for-file-creation/9553/4 "2024-07-03T09:11:33Z")
Hi Excuse me Added ions ---
**Author:** ![m.m](https://avatars.discourse-cdn.com/v4/letter/m/958977/32.png) [@m.m](https://gromacs.bioexcel.eu/u/m.m)\ **Post date:** [July 3, 2024, 9:20am UTC](https://gromacs.bioexcel.eu/t/fix-error-for-file-creation/9553/5 "2024-07-03T09:20:09Z")
Hi Creates a solvent ---
**Author:** ![m.m](https://avatars.discourse-cdn.com/v4/letter/m/958977/32.png) [@m.m](https://gromacs.bioexcel.eu/u/m.m)\ **Post date:** [July 3, 2024, 11:38am UTC](https://gromacs.bioexcel.eu/t/fix-error-for-file-creation/9553/6 "2024-07-03T11:38:37Z")
The above problem is fixed but still it doesn’t create the em .gro file. ---
**Author:** ![m.m](https://avatars.discourse-cdn.com/v4/letter/m/958977/32.png) [@m.m](https://gromacs.bioexcel.eu/u/m.m)\ **Post date:** [July 3, 2024, 11:41am UTC](https://gromacs.bioexcel.eu/t/fix-error-for-file-creation/9553/7 "2024-07-03T11:41:22Z")
The DNA receptor is alone ---
**Author:** ![asif2](https://avatars.discourse-cdn.com/v4/letter/a/3da27b/32.png) [@asif2](https://gromacs.bioexcel.eu/u/asif2)\ **Post date:** [July 3, 2024, 2:11pm UTC](https://gromacs.bioexcel.eu/t/fix-error-for-file-creation/9553/8 "2024-07-03T14:11:19Z")
so did you tried as above ? and are you still facing the same error? ---
**Author:** ![m.m](https://avatars.discourse-cdn.com/v4/letter/m/958977/32.png) [@m.m](https://gromacs.bioexcel.eu/u/m.m)\ **Post date:** [July 7, 2024, 7:35am UTC](https://gromacs.bioexcel.eu/t/fix-error-for-file-creation/9553/9 "2024-07-07T07:35:05Z")
NO, Thank you ---
**Author:** ![asif2](https://avatars.discourse-cdn.com/v4/letter/a/3da27b/32.png) [@asif2](https://gromacs.bioexcel.eu/u/asif2)\ **Post date:** [July 7, 2024, 8:33am UTC](https://gromacs.bioexcel.eu/t/fix-error-for-file-creation/9553/10 "2024-07-07T08:33:47Z")
it does not generate em.gro file as such after the solvation step pls neturalize the system using > gmx grompp -f ions.mdp -c your previous step output.gro -p topol.top -o ions.tpr > gmx genion -s ions.tpr -p topol.top - conc 0.1 -neutral -o neutralized.gro > select: 15 (sol) now do energy minimization so you will get the em.gro file which you are expecting