MOLMOD variables

Author: dkotzamp

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.
 </a>
 <a class="prompt prompt-attention">
-  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.
 </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>
@@ -362,7 +365,7 @@ one at each end of the peptide sequence, before capping.
 Capping is performed with:
 
 <a class="prompt prompt-cmd">
-python3.10 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.