# Go Martini simulation of trans-membrane protein- coordinate number mismatch error

**URL:** <https://gromacs.bioexcel.eu/t/go-martini-simulation-of-trans-membrane-protein-coordinate-number-mismatch-error/9313>\
**Category:** User discussions\
**Tags:** mdrun\
**Created:** [June 5, 2024, 1:01pm UTC](https://gromacs.bioexcel.eu/t/go-martini-simulation-of-trans-membrane-protein-coordinate-number-mismatch-error/9313 "2024-06-05T13:01:09Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Rudhra](https://avatars.discourse-cdn.com/v4/letter/r/958977/32.png) [@Rudhra](https://gromacs.bioexcel.eu/u/Rudhra)\
**Post date:** [June 5, 2024, 1:01pm UTC](https://gromacs.bioexcel.eu/t/go-martini-simulation-of-trans-membrane-protein-coordinate-number-mismatch-error/9313/1 "2024-06-05T13:01:09Z")

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GROMACS version:  
GROMACS modification: Yes/No  
Here post your question

Hi, All  
I wanted to perform go martini simulation for my transmembrane protein with lipid bilayer. During energy minimisation step I got coordinate number mismatch error.

 ![error](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/b/b823071163352b5dfc24b6f732c8414c71a488bc.png)

Approximately 377 more atoms are present in my system topology file than in my coordinate file (system.fix.gro). I repeated the simulation three times over. However, I continue to receive this problem.

This was the command-line i have followed  
gmx editconf -f 7CW4\_cg.pdb -o 7CW4\_cg.gro -box 22 22 22 -bt cubic -rotate 0 360 270  
insane -f 7CW4\_cg.gro -o system.gro -p topol.top -pbc square -box 28,28,25 -l POPC:20 -l POPE:3 -l CHOL:4 -center -sol W -charge auto -dm -0.1 -d 1 -salt 0.15  
gmx make\_ndx -f system.gro -o index.ndx  
gmx editconf -f system.gro -o system-fix.gro -n index.ndx  
gmx grompp -p system.top -c system-fix.gro -f minimization.mdp -o minimization.tpr -r system-fix.gro  
gmx mdrun -deffnm minimization -v

Here are the contents of my system.top and system.fix.gro files:  
[system.top](https://gromacs.bioexcel.eu/uploads/short-url/r1zjliazvf9xWTGQWj6Fp5drTAT.top) (585 Bytes)  
[system-fix.gro.txt](https://gromacs.bioexcel.eu/uploads/short-url/a0YujSRtxi0n4iwZbj2JuqaShFx.txt) (7.1 MB)

Can someone please give me any ideas on how to fix this error?

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**Author:** ![Karis](https://avatars.discourse-cdn.com/v4/letter/k/ed8c4c/32.png) [@Karis](https://gromacs.bioexcel.eu/u/Karis)\
**Post date:** [June 6, 2024, 7:50am UTC](https://gromacs.bioexcel.eu/t/go-martini-simulation-of-trans-membrane-protein-coordinate-number-mismatch-error/9313/2 "2024-06-06T07:50:18Z")

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You might need to check if there’s a mismatch between how many atoms your topology files and coordinate file has for each residue (I’m noticing that the number of atoms in your system topology exceeds that of the coordinate file by 377 and there happen to be 377 molecules of CHOL present, so the .itp file with CHOL might have 1 extra atom listed for each CHOL)

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**Author:** ![Rudhra](https://avatars.discourse-cdn.com/v4/letter/r/958977/32.png) [@Rudhra](https://gromacs.bioexcel.eu/u/Rudhra)\
**Post date:** [June 6, 2024, 9:02am UTC](https://gromacs.bioexcel.eu/t/go-martini-simulation-of-trans-membrane-protein-coordinate-number-mismatch-error/9313/3 "2024-06-06T09:02:42Z")

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Thanks for your reply, ma’am. I will check it.