OneAngstrom – Page 153

When You Need That Specific GROMACS Version

Reproducing published results or running benchmarks that match exactly what others have done is a common challenge in molecular modeling. One subtle but impactful issue? GROMACS version mismatches. Even minor updates to GROMACS can introduce changes in default settings, force…

Exporting Ligand Trajectories Along Unbinding Paths in PDB Format

OneAngstrom

If you work with protein-ligand systems, a common challenge is capturing the movement of a ligand along a path — for example, its unbinding from the active site — and exporting this data in a format usable for downstream tasks…

How to Find Molecules with Specific Partial Charge in SAMSON

OneAngstrom

When working with large molecular models, quickly locating structures with specific electronic properties can significantly speed up your workflow. One such case—frequently encountered in charge-based simulations, electrostatic analyses, or simply in identifying reactive species—is the need to find molecules with…

Avoiding Common Mistakes When Preparing Proteins for Docking

OneAngstrom

One of the most common sources of error in protein docking simulations is starting with an improperly prepared protein structure. Even a few misplaced atoms, missing hydrogens, or leftover water molecules can impact docking results and mislead analysis. If you’re…

Editing Atoms On the Fly While Simulating with UFF in SAMSON

OneAngstrom

Working with molecular models often involves tweaking structures to better fit expected configurations, eliminate artifacts, or explore structural variations. But what happens when you’re already mid-simulation, and you realize a modification is needed—say, removing a misplaced hydrogen, or adding a…

Saving Molecular Conformations and Trajectories with SAMSON’s Normal Modes Advanced

OneAngstrom

One common challenge in molecular modeling is capturing and comparing key conformational states during a simulation. Whether you are exploring structural flexibility, functional transitions, or designing ligands to fit various binding site shapes, keeping track of conformational changes is crucial.…

Quickly Find (or Hide) Molecules in Complex Scenes with NSL

OneAngstrom

When working with large molecular systems — think thousands of atoms, many chains, or dense biomolecular assemblies — navigating, selecting, and editing specific parts of a scene can be time-consuming. If you’ve ever spent minutes clicking through structures to find…

Selecting Visual Presets in SAMSON: A Quick Guide with the NSL

OneAngstrom

When working on molecular models in SAMSON, visualization is often more than just aesthetics—it’s essential. Different render presets can highlight atomic structures, interaction networks, or molecular surfaces, which all help communicate scientific insight effectively. But when projects become complex, selecting…

Creating Smooth Transitions Between Protein Conformations with ARAP Interpolation

OneAngstrom

When studying protein dynamics, researchers often encounter an important question: how do we realistically interpolate between two known conformations of a protein structure? Whether you’re setting up umbrella sampling simulations or exploring conformational transitions for molecular docking, creating a smooth…

Quickly Explore Molecular Variants with Positional Analogue Scanning in SAMSON

OneAngstrom

When designing new drug candidates or optimizing a lead compound, molecular modelers often face the challenge of evaluating how small chemical modifications affect binding affinity, selectivity, or physicochemical properties. One effective approach to address this is positional analogue scanning, where…