GROMACS version: 2024
GROMACS modification: Yes/No
Here post your question: Hello so, I have an error with the coordinate files. I first made a membrane from charmmgui, then i equilibrated it and then I had a pdb file from step7_production, to visualize, this is a bacterial membrane (popg, popc, tocl). then I had to do peptide membrane Simulation. I made a peptide str. from PEPFOLD4.0, my peptide is 7aa in length. I placed the peptide at the surface of my equilibrated membrane in PYMOL, I saved this and then I wanted to run MD. i generated a gro file for my peptide + membrane system which i called as system.gro, I also updated my topol file with the peptide name under molecules section. after running this: “gmx grompp -f minim.mdp -c system.gro -p topol.top -o em.tpr”. I am getting this error: Fatal error: number of coordinates in coordinate file (system.gro, 27037) does not match topology (topol.top, 27195). can you pls help me with this if possible.
You have 158 atoms more in your topology that in your gro file. It should be straighforward by looking into the files to figure out what causes the mismatch.
hello, I did look into the files, but i fail to understand how to make the atoms match, i am also new to all gmx commands and outputs. I cannot understand why is there a difference, can someone pls guide me
158 atoms is of the size of your 7-residue peptide. My first guess would be that you do not have your peptide in the gro file you passed to grompp.
so it shows in my gro file, which is the membrane+peptide known as system.gro file, my peptide is visible with its atoms in that gro file, still the error, should i attach my files here?
Maybe the easiest way is to run gmx make_ndx on you gro file. Then you can see the counts of atoms in different groups (protein, water, …). Then you can compare with the system section in your top file.