GROMACS version:
GROMACS modification: Yes/No
Here post your question Hi
I have a .gro file of a protein from which on pymol I mutated a residue from GLN to ALA. Using the same topology (to avoid doing the parameterisation of the ligand inside the protein again) when I need the ions.trp file it gives me this error. I think it is the 2 water molecules that are missing in the .gro file in the mutation from gln to ala that do not match the number of atoms in the topology. I added them to the .gro file and it works, it no longer gives me an error. The coordinates I entered are made up. My question is do you know where I can get real coordinates of the 2 water molecules that are missing? Is it possible to do something like this?
Thanks
Dear @C18
Sorry do you mean that you when you try to compile the tpr file you get the error? And as input you are using the .gro file that comes from the pymol mutation wizard? What did you mean with the fact that you are keeping the same topology? If you mutated the protein, it’s topology will change.
I thought I could use the same topology because the protein was the same but with one mutation you’re right I don’t think I can do this because the topology is different.
thank you
No by definition if you mutate a residue then the protein is not the same, but the it is the mutant. You have to go a step back and generate the new .itp file for the protein!