Anwesh Pandey Dr Thirumal Kumar D Aliyu Adamu I tried the above suggested Gromacs and Charmm36 forcefield to conduct the simulation of my docked protein. My residue S-adenosyl methionine (SAM) in the protein is designated as UNK in the docked file. But when I tried to create topology file for the docked protein, I got a fatal error. Residue 'UNK' not found in residue topology database
Also a Warning: No residues in chain starting at UNK1 identified as Protein/RNA/DNA.
This makes it impossible to link them into a molecule, which could either be
correct or a catastrophic error. Please check your structure, and add all
necessary residue names to residuetypes.dat if this was not correct.
Problem with chain definition, or missing terminal residues.
This chain does not appear to contain a recognized chain molecule.
If this is incorrect, you can edit residuetypes.dat to modify the behavior.
look for gromacs_charmm tutorial in my RG account, there you'll find steps. However you need to bring uniformity in your labeling of ligand, perhaps it should be LIG instead of UNK. Try and then let us know.
Anwesh Pandey I changed my ligand name to SAM. Still the error is the same. Please look into it. I am not being able to create the protein topology with the command pdb2gmx
Suprim Tha I expect SAM is the name for your ligand in the file. If your system involving both protein and ligand, you have to generate the ligand topology using third parties. You may refer to the following tutorial.