Protein-ligand complex tutorial errors

User discussions
1

GROMACS version:2023
GROMACS modification: Yes/No
Hello,
I am a new user and tried to run a simple md simulation according to the protein ligand complex tutorial of gromacs. I edited the 3HTB pdb file, as the tutorial mentions.
Specifically, i run:

  1. grep JZ4 3HTB_clean.pdb
  2. grep -v HETATM 3HTB_clean > 3htb_processed.pdb
  3. gmx pdb2gmx -f 3htb_processed.pdb -o 3htb_processed.gro
    Then i choose CHARMM all-atom force field (which i downloaded and extracted to /gromacs/share/gromacs/top/) according to the tutorial, but i keep getting Fatal Errors such as:
    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
    Fatal error:
    Residue ‘HID’ not found in residue topology database
    I keep editting atomtypes.atp and aminoacids.rtp at the specific force field, but i wonder what am i doing wrong.
    Thank you very much for your time
2

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

3

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.

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

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).

4

Thank you very much, that fixed my problem!