While performing Protein-Ligand interaction in Gromacs version 2021 using the command line: gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr. I encountered this Fatal error: number of coordinates in coordinate file (solv.gro, 29336) does not match topology (topol.top, 54674).
I want to know how can I solve and correct this mismatch?
I am attaching both the files of topology (topol.top) and solv.gro
Thanks
Hi Fatima Mourabiti ,
It is rather strange that the difference between the top and gro file is huge.
Based on the numbers alone, it appears that there might be additional solvent atoms (~25k) in the top file.
So there is a chance that the solvation step was done twice instead of once.
The somewhat quick solution is to redo from the initial step since it is still in the initial stages, and of course be careful this time round.
All the best.
Thank you for your answer, I redid it from the initial step but I still have the same problem but without a huge difference between the two files;
Fatal error:
number of coordinates in coordinate file (solv.gro, 28697)
does not match topology (topol.top, 28711).
THANK YOU
There isnt much to go on with the information provided.
However here are some solutions solved by others (by Google-ing):
https://gromacs.bioexcel.eu/t/number-of-coordinates-in-coordinate-file-does-not-match-topology/5230/7
https://www.researchgate.net/post/How-to-correct-the-number-of-coordinates-in-coordinate-file-if-it-does-not-match-the-topology-in-Gromacs
https://gromacs.bioexcel.eu/t/number-of-coordinates-did-not-match-in-coordinated-file-with-the-topology-file/1931/13
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