I’m reproducing this tutorial Lysozyme in Water with a different protein.
During the generation of the .tpr file for the step of adding ions, I’m getting this error: ‘No such molecule type SOL.’ After adding the SOL to the molecule type section, I get the ‘molecule type protein has no atoms’ error.
My protein has a covalently bonded cofactor, so I’ve used AMBER files () for the generation of GMX.top and protein.gro files and started the tutorial from the ‘define box and solvent’ step.
I’m providing relevant parts of the topology file:
[ moleculetype ]
[ system ]
protein in water
[ molecules ]
; Compound nmols
Any help is appreciated!