Protein-ligand complex tutorial errors

[jalemkul]

@EOrfanakis

Fatal error:
atom C1 not found in buiding block 1MET while combining tdb and rtp
Fatal error:
Atom type H1 (residue MET) not found in atomtype database

The tutorial uses a slightly older version of the CHARMM36 port that did not have a certain terminal patch that screws up methionine. You need to interactively select the NH3+ terminus type with -ter added to the pdb2gmx command.

@EOrfanakis

I keep editting atomtypes.atp and aminoacids.rtp at the specific force field, but i wonder what am i doing wrong.

You should not have to make any changes to force field files.

@jjmllen

you need to prepare your protein first either use MOE or Swiss pdb viewer

This is unnecessary. The tutorial should work cleanly without any real extra effort with outside programs. I will probably update it soon for those users who are using the July 2022 CHARMM36 port. The tutorial uses one from March 2019 (which is still available online, so the tutorial can be completed as written).