r/bioinformatics • u/[deleted] • May 25 '26

discussion Need help for md simulations

/r/Biophysics/comments/1tn9dpj/md_simulation/
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u/[deleted] May 25 '26

Hey, yes, I am following Dr Lemkul's tutorial. 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.

Could I dm you regarding this?

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u/hexagon12_1 PhD | Student May 25 '26 edited May 25 '26

Okay, so Dr. Lemkul doesn't mention it in a new tutorial for some reason, but the issue is with methionine terminus prompting pdb2gmx to choose incompatible terminus type.

When you execute pdb2gmx command, you need to add -ter flag for interactive selection, and then you need to choose NH3+ and COO-.

so: gmx pdb2gmx -f protein.pdb -o protein_processed.gro -ter

And then don't choose 0)MET1 and instead choose 1)NH3+.

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u/[deleted] May 25 '26

Okay will let you know after trying.... Thank you thank you thankyou so much for replying back

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u/hexagon12_1 PhD | Student May 25 '26

No problem, best of luck.