If you are doing work on Ligand-Protein Complex, then first of all goto your manually made .gro file (it may be named as complex.gro or conf.gro).

At the top of that .gro file you will find a total number, you have to change that number according to your newly added ligand's total number.

Like if you have 4000 protein in total and you added another 30 ligand into your .gro file the actual number would be 4030 at the top of that .gro file.

Thank you.

grompp expects the number of .gro coordinates based on [ molecules ] directive in .top file. You should check, if the numbers correspond. The difference between your actual and expected number is divisible by 3, so I assume, the number of SOL molecules in [ molecules ] directive should be corrected.

beside the residue (molecule) definition in the .top file, at the end of file there is a list of molecules and number of them in the box. Probably this numbers do not match you .gro file (and as Michal said, most probably your number of solvents is the source).

if you modified the topology file for adding a ligand topology please check that each atom in the ligand topology match each atom in the .gro file

I think that is the problem

I had the same issue, here is the solution.

Error: The number of coordinate files (22573) doesn't match the number in the topology files (22570).

Solution: Go to your topol.top file and scroll down to the end where you will find the number of SOL molecules.

Simply increase or decrease the number according to your situation but remember, changing 1 number counts for 3. So, in my case i just increased one number and it worked. I increased the number of SOL molecules from 9336 to 9337.

Good luck

If you are doing work on Ligand-Protein Complex, then first of all goto your manually made .gro file (it may be named as complex.gro or conf.gro).

At the top of that .gro file you will find a total number, you have to change that number according to your newly added ligand's total number.

Like if you have 4000 protein in total and you added another 30 ligand into your .gro file the actual number would be 4030 at the top of that .gro file.

Thank you.

Hello everyone,

I am getting the same issue but the issue is odd. I checked trough the pdb file and the gro file. the number of atoms is correct. however, the top file gives an error by two atoms. anybody else had the same issue? is there a system of adding some dummy atoms?

@Ayesha Fatima you can use swiss pdb viewer tool to correct missing atoms

If you are sure on your chl.gro file after gmx pdb2gmx, I think you have to redo other steps again I remember I had the same problem but after making a new box everything was ok. (I checked your gro file and CHL molecule had some missing atoms)

hello everyone

how to solve this issue

"Reaction Preview Error Fixed atom coordinate mismatch. Fixed atom coordinates should match to within 0.0010"

Hi people, I am facing this issue and I am unable to proceed, Any guidance will be appreciated :

Fatal error:

number of coordinates in coordinate file (solv.gro, 504056)

does not match topology (topol.top, 504058)

Aamir Mehmood In my case, the difference is of 2, Can you tell me whats the issue here ? Thanks