Text here about NGLView
This view looks a bit messy. MDAnalysis has a human readable selection syntax
that allows us to isolate parts of our structure. We will take our MDAnalysis Universe (the variable u) and use the select_atoms function.
@@ -506,7 +508,7 @@
Upon viewing this structure, you will notice that our ligand seems to appear twice. If you open the PDB file to investigate, you will see the following in the ligand section:
@@ -544,7 +546,7 @@When we inspect the ligand in the binding site, we notice a few things. First, the binding site has a large hydrophobic area on the surface. @@ -578,7 +580,7 @@
/usr/share/miniconda/envs/biochemist-python/lib/python3.11/site-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'formalcharges' Using default value of '0'
+/home/janash/miniconda3/envs/biochemist-python/lib/python3.11/site-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'formalcharges' Using default value of '0'
warnings.warn("Found no information for attr: '{}'"
@@ -601,12 +603,12 @@ Structure Preparation
INFO:PDB2PQR v3.6.2: biomolecular structure conversion software.
INFO:Please cite: Jurrus E, et al. Improvements to the APBS biomolecular solvation software suite. Protein Sci 27 112-128 (2018).
-INFO:Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
-INFO:Checking and transforming input arguments.
-INFO:Loading topology files.
-INFO:Loading molecule: pdb/protein_2zq2.pdb
+INFO:Please cite: Dolinsky TJ, et al. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35 W522-W525 (2007).
+INFO:Checking and transforming input arguments.
+INFO:Loading topology files.
+INFO:Loading molecule: pdb/protein_2zq2.pdb
ERROR:Error parsing line: invalid literal for int() with base 10: ''
ERROR:<REMARK 2>
ERROR:Truncating remaining errors for record type:REMARK
@@ -669,9 +671,7 @@ Structure Preparation
-
-
INFO:Applying force field to biomolecule states.
-INFO:Regenerating headers.
+
+
+
-
----------------------------------------------------------------------------
-OSError Traceback (most recent call last)
-Cell In[14], line 5
- 1 from rdkit import Chem
- 3 from rdkit.Chem.AllChem import AssignBondOrdersFromTemplate
-----> 5 template = Chem.MolFromMol2File("ligands/13U_ideal.mol2")
- 6 pdb_ligand = Chem.MolFromPDBFile(f"pdb/ligand_A.pdb")
- 8 template = Chem.RemoveAllHs(template)
-
-OSError: Bad input file ligands/13U_ideal.mol2
-
-
-
-[17:30:37] WARNING: More than one matching pattern found - picking one
+[23:04:16] WARNING: More than one matching pattern found - picking one
@@ -799,7 +787,7 @@ Visualizing the Binding Site
-/home/janash/miniconda3/envs/iqb-2024/lib/python3.11/site-packages/MDAnalysis/converters/RDKit.py:473: UserWarning: No `bonds` attribute in this AtomGroup. Guessing bonds based on atoms coordinates
+/home/janash/miniconda3/envs/biochemist-python/lib/python3.11/site-packages/MDAnalysis/converters/RDKit.py:473: UserWarning: No `bonds` attribute in this AtomGroup. Guessing bonds based on atoms coordinates
warnings.warn(
@@ -828,7 +816,7 @@ Visualizing the Binding Site
-
+