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charmm36 ff requirement for gmx pdb2gmx #758

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dkotzamp merged 3 commits into from
Jan 10, 2026
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charmm36 ff requirement for gmx pdb2gmx #758

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charmm36 ff requirement for gmx pdb2gmx
dkotzamp Jan 9, 2026
c6d1899
Update simulation.md
dkotzamp Jan 9, 2026
a0dfa7a
MOLMOD variables
dkotzamp Jan 9, 2026
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9 changes: 8 additions & 1 deletion education/molmod_online/simulation.md
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Expand Up @@ -318,6 +318,13 @@ This choice is usually limited by the force field, unless there is a specific ne
<a class="prompt prompt-info">
Generate a topology and matching structure for the p53 peptide with GROMACS.
</a>
<a class="prompt prompt-attention">
Make sure the folder charmm36-jul2022.ff/ is present in your current working directory before running pdb2gmx.
When you run the command, GROMACS will prompt you to choose a force field - charmm36-jul2022 should appear as option 1.
</a>
<a class="prompt prompt-cmd">
cp -r $MOLMOD_DATA/charmm36-jul2022.ff .
</a>
<a class="prompt prompt-cmd">
gmx pdb2gmx -f p53_helix.pdb -o peptide.gro -p peptide.top -ignh -ter
</a>
Expand Down Expand Up @@ -358,7 +365,7 @@ one at each end of the peptide sequence, before capping.
Capping is performed with:

<a class="prompt prompt-cmd">
python pdb_cap.py --pdb peptide_helix.pdb --cap
python3.10 $MOLMOD_BIN/pdb_cap.py --pdb peptide_helix.pdb --cap
</a>

The script produces a new file named peptide_helix_capped.pdb, which should then be used as input for pdb2gmx.
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