When I was simulating my protein, "Fatal error: Atomtype LC3 not found" had occured. I checked my force field atom type and it contains LC3 with correct parameters. Before this error I used inflategro perl script. What may cause this problem?
Hi Anastasia! If you find your atom in atomtypes.atp this error can occur anyway. Normally, it means that your file ffnonbonded.itp does not contain L-J parameters for this atom type. If you have a folder forcefield.ff in your simulation folder you shall edit the file ffnonbonded.itp by manually adding L-J parameters for this atom type.
I got the same error but for CCL4. I checked in both atomtypes.atp and ffnonbonded.itp. CCL4 is there in both files But how to add L-J parameters for this atom type? kindly reply?