GROMACS error

Question

[ali.kian.saei]

I face this error when I want use this command:

gmx grompp -f ions.mdp -c complex-solv.gro -p topol.top -o ions.tpr -maxwarn 1

error

Fatal error:
number of coordinates in coordinate file (complex-solv.gro, 168195)
             does not match topology (topol.top, 168243)

How can I solve this error?

[manaswwm]

IMO it is very tough to judge from the limited information that you have given here to understand the error. However, from the error line it looks as if your topology file contains information on more atoms (I am guessing a small ligand molecule) than what is included in your structure file. It would help to just compare your topology file and structure file side-by-side.

Answer 1

[Pappu]

You need to adjust the topol.top to match the total number of atoms in the gro file. I guess it has extra ions which is not in the gro file.