diff --git a/education/molmod_online/simulation.md b/education/molmod_online/simulation.md index 47537a6c..281731a4 100644 --- a/education/molmod_online/simulation.md +++ b/education/molmod_online/simulation.md @@ -318,6 +318,13 @@ This choice is usually limited by the force field, unless there is a specific ne Generate a topology and matching structure for the p53 peptide with GROMACS. + + 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. + + +cp -r $MOLMOD_DATA/charmm36-jul2022.ff . + gmx pdb2gmx -f p53_helix.pdb -o peptide.gro -p peptide.top -ignh -ter @@ -358,7 +365,7 @@ one at each end of the peptide sequence, before capping. Capping is performed with: -python pdb_cap.py --pdb peptide_helix.pdb --cap +python3.10 $MOLMOD_BIN/pdb_cap.py --pdb peptide_helix.pdb --cap The script produces a new file named peptide_helix_capped.pdb, which should then be used as input for pdb2gmx.