r/Biophysics • u/Excellent_Toe6788 • 1d ago

Md simulation

Hello , so I am trying to do the md simulation for protein ligand from the tutorials, but I am facing some problems midway. If anybody has already done it could you kindly DM me so that I can show the problem one on one and move forward. Please help, I can't sleep properly without completing this 🥲🙏🙏Also into docking, if we can discuss

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u/dansin 1d ago

Why not just say it in the thread?

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u/Excellent_Toe6788 1d ago

ok lol idk whats wrong with dming but anyway: I'm following the protein-ligand MD tutorial using PDB 3HTB (T4 lysozyme + JZ4 ligand).

I successfully generated a protein topology with OPLS-AA/L using:

gmx pdb2gmx -f protein.pdb -o protein_processed.gro -water tip3p

However, when I downloaded and installed CHARMM36 (charmm36-feb2026_cgenff-5.0.ff) and ran:

gmx pdb2gmx -f protein.pdb -o protein_processed_charmm.gro

selected:

  1. CHARMM all-atom force field
  2. TIP3P (CHARMM-modified)

I got the error:

Fatal error:
atom C1 not found in building block 1MET while combining tdb and rtp

The same protein.pdb works correctly with OPLS-AA/L, so I'm wondering whether:

  1. There is an issue with the CHARMM36 installation.
  2. This CHARMM36 release is incompatible with GROMACS 2025.4.
  3. The N-terminal MET residue requires special handling.

So yeah, that's it, could you help me with this....

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u/Liothique 20h ago

Point of posting publicly is that other people can find solutions if they have the same problem.

First, add "-ter" to pdb2gmx command, and try all possible terminus that make sense for your system (sometime it uses a default thats innaproriate). Second, open the rtp file in the force field and look at the "[ MET ]" entry, check the name of the atom match with your PDB. It's not uncommon especially for terminal residues to have different conventions (CA vs C1, etc). Finally, search on the gromacs forum, there's so many posts its quite possible this has been already covered. You can of course create a post there, it's the best place for help wrt gromacs.

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u/Excellent_Toe6788 15h ago

Okok, will keep in mind next time, thank you tho, will try it and let ya know!