#32 protein-ligand-cofactor system README

README.md

@@ -524,11 +524,11 @@ To calculate the affinity between a protein-cofactor system and a ligand, use `-
 By default, StreaMD uses 'UNL' as the ligand system residue name, but it is recommended to verify the exact residue name in the _all_ligand_resid.txt_ file.
 Additionally, specify `--append_protein_selection 'CFR'` to include cofactor into the protein system for the calculations (you can find the exact cofactor residue name also in the _all_ligand_resid.txt_ file).
 ```
-run_gbsa  --wdir_to_run md_files/md_run/protein_H_HIS_ligand_1 md_files/md_run/protein_H_HIS_ligand_2  --append_protein_selection ZN GDP
+run_gbsa  --wdir_to_run md_files/md_run/protein_H_HIS_ligand_*  --append_protein_selection MG GTP
 ```
-To calculate binding free energy for the protein system and the cofactor, use `--ligand_id 'CFR'` instead.
+To calculate binding free energy between the protein system and the cofactor, use `--ligand_id 'CFR'` instead.
 ```
-run_gbsa  --wdir_to_run md_files/md_run/protein_H_HIS_ligand_1 md_files/md_run/protein_H_HIS_ligand_2  --append_protein_selection ZN --ligand_id GDP
+run_gbsa  --wdir_to_run md_files/md_run/protein_H_HIS_ligand_*  --append_protein_selection MG --ligand_id GTP
 ```
 
 
@@ -600,11 +600,11 @@ To obtain interaction fingerprints between a protein-cofactor system and a ligan
 By default, StreaMD uses 'UNL' as the ligand system residue name, but it is recommended to verify the exact residue name in the _all_ligand_resid.txt_ file.
 Additionally, specify `--append_protein_selection 'CFR'` to include cofactor into the protein system for the calculations (you can find the exact cofactor residue name also in the _all_ligand_resid.txt_ file).
 ```
-run_prolif  --wdir_to_run md_files/md_run/protein_H_HIS_ligand_1 md_files/md_run/protein_H_HIS_ligand_2 --append_protein_selection 'ZN'
+run_prolif  --wdir_to_run md_files/md_run/protein_H_HIS_ligand_* --append_protein_selection MG GTP
 ```
 To calculate interaction fingerprints between protein system and cofactor, use `--ligand_id 'CFR'` instead.
 ```
-run_prolif  --wdir_to_run md_files/md_run/protein_H_HIS_ligand_1 md_files/md_run/protein_H_HIS_ligand_2  --ligand_id 'CFR'
+run_prolif  --wdir_to_run md_files/md_run/protein_H_HIS_ligand_*  --ligand_id 'GTP'
 ```
 
 #### **Output**