OneAngstrom – Page 118

Why Your Molecular Files Won’t Open — And How to Fix It in SAMSON

If you’ve ever tried to open a structure file in your molecular modeling software and been met with a blank screen or an error message, you’re not alone. Molecular modelers often work with a wide variety of file formats—PDB, mmCIF,…

How Node Group Attributes Can Help You Organize Molecular Models Better

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When working on complex molecular models, it doesn’t take long before your document becomes cluttered with atoms, residues, molecules, and larger structural elements. One underused — but highly effective — way to keep things organized in SAMSON is by leveraging…

From Clicks to Code: Writing Python Scripts with SAMSON AI

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When working on molecular modeling projects, many researchers face a common challenge: repetitive, manual tasks that cost time and lower reproducibility. Whether it’s translating structures, computing simple properties, or automating a workflow, scripting offers a way out—if you know how…

Drawing Nanotubes with a Mouse: Interactive CNT Modeling in SAMSON

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Molecular modelers working with carbon nanotubes (CNTs) often need to generate structures quickly to test ideas, verify hypotheses, or initiate simulations. However, many tools place barriers such as command-line syntax, abstract parameters, or pre-baked models that don’t reflect exact needs.…

Running GROMACS Simulations in the Cloud with SAMSON

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One common challenge for molecular modelers is performing large-scale or lengthy GROMACS simulations without overloading their local machines. Interactive work becomes sluggish, fans spin up, and background simulations may suddenly halt if the system goes idle or reboots. What if…

Avoiding Pitfalls in Coarse-Grained MD: Setting Up Solvents and Ions Correctly

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One of the most overlooked yet crucial steps in preparing coarse-grained molecular dynamics (MD) simulations is solvent and ion setup. If coarse-grained (CG) models are incorrectly solvated or ionized, simulations often produce unrealistic results—or fail entirely. This blog post focuses…

Working Smarter with Editors in SAMSON

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Molecular modeling can often feel repetitive when tasks like structure modification, selection, transformation, or even simple visualization require many manual steps. If you’ve ever wished there was a faster, more intuitive way to interact with your models—perhaps even generate nanotubes…

Filtering Structural Groups by Partial Charge in SAMSON

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When analyzing molecular structures, it’s often essential to isolate specific components based on their electrostatic properties. One such useful property is the partial charge. Whether you’re studying intermolecular interactions, preparing calculations, or creating educational models, being able to efficiently find…

Organize Molecular Structures Effortlessly with Folders in SAMSON

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Managing complex molecular models—especially those involving large biomolecular systems, multiple ligands, or reference structures—can become overwhelming. Most molecular modelers have faced the frustration of cluttered data views, accidentally hiding key elements, or applying actions to unintended parts of a model.…

Why You Should Minimize Your Ligands Before Docking

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If you’ve ever docked a ligand library and received unimpressive binding poses, misleading scores, or just downright strange conformations, there’s a high chance the source was not AutoDock Vina itself—but the ligands you fed into it. One of the most…