Error in the coordinate file sol.gro and topol.gro

User discussions
, , , ,
1

Hello, i’m facing this issue

Program: gmx grompp, version 2024.2
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 706)

Fatal error:
The number of coordinates in the coordinate file (solv.gro, 1,136,228)
does not match the topology (topol.top, 1,136,229)

In the topology file, it indicates SOL = 377,542.

I checked the solv.gro file, which starts with 2SOL and ends with 77,543SOL. When I subtract 77,541, I replace it in the topology file, but the process still doesn’t work, and I get the same error. Am I missing something here? Here i provide the file in text format WITHOUT ANY MODIFICATIONS.

File

2

Do the number of atoms listed in LIG.itp match what is listed for LIG in the .gro file?

Regarding the number of SOL, everytime the residue number (the # in #SOL) reaches 99999SOL, the next residue reverts back to 0SOL, so the number of SOL molecules should be correct, and there doesn’t seem to be a mismatch between the number of atoms in the protein chain, which leaves the ligand