I am doing MD simulation with OPLS-AA forcefield for protein_ligand system. The ligand is parameterized by webtools LigGenPar.
I am adding ions to the system after solvate step. When running command: “gmx grompp -f em.mdp -maxwarn 1 -c rec_1.pdb -p top.top -o ion.tpr”, I get an error “number of coordinates in coordinate file (rec_1.pdb, 64028) does not match topology (top.top, 83533)
(image below)”
I have checked my system information as follows:
Protein has 5463 atoms
Ligand has 50 atoms
System added 19505 water molecules
So the total number of atoms in my system is 64028 atoms (corresponding to the number of atoms in red_1.pdb file). However, I don’t understand why my top.top file has 83533 atoms? (83533 = 64028+19505?)
I have attached my top.top files. I hope someone can suggest me other option or how to fix this error. If you want me to send more information about another file, please leave me a comment.
Thanks a lot in advance
The number of atoms seems to point at a problem with water, as the mismatch is exactly the number of solvent molecules. In particular, your topology points to a 4-points water model (tip4p.itp). Did you solvate with a 3-points water model? This might explain the difference. You can fix this firstly by finding out if you need a 3 or 4 points water model and then, if 3, point the topology to the correct 3-points model, and if 4 re-solvate the box with a 4-points water model (gmx solvate -cp tip4p.gro ... should do the job).
