For small, charged molecules, you can choose the "ion" component type.For small molecules in low concentrations (To facilitate building non-water and mixed-solvent systems, Multicomponent Assembler uses three different packing strategies: However, if you try the approach shown previously with small molecules in high concentration, you may find that it is very difficult and time-consuming to pack non-water solvent molecules at realistic concentrations. The same approach allows us to combine free-floating nanomaterials and small molecules. In the previous videos, we combined soluble proteins with membrane-like materials and membrane proteins. 7: Building Mixed Protein-Ligand Systemsįiles used in this demo download.tgz Video Transcript.6: Custom Solvent Composition, Gaseous Solvents.5: Building Nano-Bio Interface with Image Bonds.4: Solvating Proteins with Membrane-like Polymers or Pre-Equilibrated Membranes.3: Solvating Proteins with Membranes and Membrane Proteins.9: Modeling Carbonaceous materials (CNT & Graphite).8: Modeling Molybdenum Disulfide (MoS 2).7: Modeling Surfaces and Nanocrystal of Hydroxyapatite.6: Modeling Nanoparticle and Surfaces of Silica.5: Building Surface of Cement Mineral (Tricalcium Silicate).3: Building Clay Mineral Model (Montmorillonite).2: Surface and Wulff construction of Fcc metal (Au).4: A Melt System: Phase Behavior of PS 100-b-PMMA 100.3: A Solution System: Self-Assembly of PEO 40PEE 37.7: Relative Ligand Binder for Membrane Systems.6: Absolute Ligand Binder for Membrane Systems.5: Relative Ligand Binder for Solution Systems.4: Absolute Ligand Binder for Solution Systems.2: Building a fully-glycosylated SARS-CoV-2 S in complex with ACE2.1: Building a fully-glycosylated full-length S protein in a viral membrane (6VSB, 6VXX).3: Changing Protonation State with PDB2PQR and reading AMBER FF residue names (6IYC).2: Preparation of protein/DNA/RNA complex for Amber FF (6O0Z).1: Preparation of protein/N-glycan/ligand/membrane complex for Amber FF (5O8F).4: Solution system of a heparan sulfate molecule (1AXM).3: Membrane system of a cholera toxin B and ganglioside GM1 complex (3CHB).2: Modeling N-glycans on a Fc heterodimer of IgG (5TPS).1: Solution System of HIV Envelope Protein (5FYL).1: General Ligand Reading Strategy (186L, 2OI0).5: Oligomerization and Spin Labeling (2OMF).
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3: Renaming and Missing Residues (5U4J, 5JY6).1: Introduction to PDB Reader (2HAC, 1KDX).