SAMSON Blog – Page 708

Avoid Rework: How to Auto-Fill Input Files for NVT Equilibration in SAMSON

When working with molecular dynamics simulations using GROMACS, setting the correct input files for each step is crucial. Whether you’re handling a protein-ligand complex, a solvated biomolecule, or a batch of systems, ensuring pipeline continuity can be tedious. One commonly…

Using NSL to Control Note Visibility in SAMSON

OneAngstrom

As molecular models grow in size and complexity, modelers often turn to visual annotations—such as notes and labels—to document observations, mark points of interest, or organize a workspace. However, with many notes cluttering the screen, one common challenge emerges: how…

Creating Smooth Protein Transition Paths with ARAP Interpolation

OneAngstrom

When modeling molecular processes, capturing transitions between different conformations of a protein is often essential. Whether you’re exploring activation pathways, refining docking poses, or setting up umbrella sampling simulations, intermediate structures along these conformational paths are a valuable resource. But…

Should You Minimize Ligands Before Docking? Here’s What Happens If You Do (Or Don’t)

OneAngstrom

When preparing ligands for docking, one question consistently puzzles molecular modelers: should ligands be minimized beforehand? The answer might not be as universal as you think, but understanding the trade-offs can improve your docking reliability and save you hours of…

Entering NOESY-based distance restraints in NMR2 (without breaking a sweat)

OneAngstrom

When modeling protein-ligand complexes from NMR data, one of the trickiest steps is translating NOESY cross-peaks into distance restraints that can be used for structure prediction. In particular, if you’re using NMR2 in SAMSON to interpret methyl-based NOESY data, you’ll…

Extracting Ligand Pathways as PDB Files: A Simple Way to Track Molecular Motion

OneAngstrom

When investigating molecular recognition, drug binding, or unbinding mechanisms, tracking how a ligand moves through a protein is crucial. However, manually extracting these trajectories into formats suitable for downstream analysis or visualization can be both tedious and time-consuming. If you’ve…

Avoid Repeating Yourself: Add Custom Index Groups Once for All Your Molecular Simulations

OneAngstrom

When preparing molecular dynamics simulations in GROMACS, many modelers use gmx make_ndx to create custom index groups. You might want to separate domains, pull particular atoms, or track specific regions of a protein. However, repeating the same selection operations for…

A Quick Guide to Selecting Backbones in SAMSON Using NSL

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When working on complex molecular systems in SAMSON, efficiently selecting specific components—like molecular backbones—is crucial. Whether you want to inspect properties, apply materials, or run analyses, the Node Specification Language (NSL) provides a clear and expressive way to specify what…

No Admin Rights? No Problem: Installing SAMSON Without Admin Privileges

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For molecular modelers working in institutional settings—especially students and researchers without administrative privileges on their workstations—software installation can be a persistent challenge. Many powerful scientific tools require admin rights, which slows down onboarding and introduces a frustrating dependency on IT…

How Sugar Molecules Hide the Coronavirus Spike (and Why That Matters for Antibodies)

OneAngstrom

If you’ve ever tried to model glycosylated proteins, you know how quickly the visual landscape becomes crowded. When it comes to the SARS-CoV-2 spike protein, which mediates viral entry into human cells, the challenge is even greater: the spike is…