From b059bae9bc74a5f5b4464b26eca61a065a71291c Mon Sep 17 00:00:00 2001 From: dkotzamp Date: Fri, 9 Jan 2026 19:14:51 +0200 Subject: [PATCH 1/3] charmm36 ff requirement for gmx pdb2gmx --- education/molmod_online/simulation.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/education/molmod_online/simulation.md b/education/molmod_online/simulation.md index 47537a6c..0c2e667a 100644 --- a/education/molmod_online/simulation.md +++ b/education/molmod_online/simulation.md @@ -318,6 +318,10 @@ 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. + gmx pdb2gmx -f p53_helix.pdb -o peptide.gro -p peptide.top -ignh -ter From c6d1899908112808cd3d170934a96c05dbd18eaf Mon Sep 17 00:00:00 2001 From: Danai Kotzampasi <57521404+dkotzamp@users.noreply.github.com> Date: Fri, 9 Jan 2026 20:22:49 +0200 Subject: [PATCH 2/3] Update simulation.md --- education/molmod_online/simulation.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/education/molmod_online/simulation.md b/education/molmod_online/simulation.md index 0c2e667a..7c9cd80d 100644 --- a/education/molmod_online/simulation.md +++ b/education/molmod_online/simulation.md @@ -362,7 +362,7 @@ 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 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. From a0dfa7a2c79230833b1ef786c0cc441a024452f5 Mon Sep 17 00:00:00 2001 From: Danai Kotzampasi <57521404+dkotzamp@users.noreply.github.com> Date: Fri, 9 Jan 2026 22:00:23 +0200 Subject: [PATCH 3/3] MOLMOD variables --- education/molmod_online/simulation.md | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/education/molmod_online/simulation.md b/education/molmod_online/simulation.md index 7c9cd80d..281731a4 100644 --- a/education/molmod_online/simulation.md +++ b/education/molmod_online/simulation.md @@ -319,9 +319,12 @@ 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. + 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 @@ -362,7 +365,7 @@ one at each end of the peptide sequence, before capping. Capping is performed with: -python3.10 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.