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

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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
error1920×1080 227 KB

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 (585 Bytes)
system-fix.gro.txt (7.1 MB)

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

2

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)

3

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