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GROMACS error

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?

gromacs topology
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updated by Ram Ram • written by ali.kian.saei • ali.kian.saei

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.

• 0 views • link
written by manaswwm manaswwm

1 answer

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.

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written by Pappu Pappu

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