Generate initial molecular configurations for MD simulations using Packmol.
npx skills add https://github.com/Hello-QM/catgo-LRG --skill packmol-hello-qm
Please help me install this Agent Skill. Skill: packmol Source: https://github.com/Hello-QM/catgo-LRG/tree/main/.claude/skills/packmol Command: npx skills add https://github.com/Hello-QM/catgo-LRG --skill packmol-hello-qm
Packmol enables automatic generation of initial molecular configurations for MD simulations by packing molecules into defined regions, saving manual setup time.
Create a solvated box by packing water.pdb and solute.pdb into a 40x40x40 Å region.
High-intent search queries and answers about installing and using this skill.
Generating initial molecular configurations for MD simulations from PDB files requires packing molecules into defined regions with specified counts and boundaries. This Skill automates that process using Packmol to build liquid boxes, mixtures, and solvated systems from your PDB or XYZ inputs.
Building a solvated liquid box with a specific solute and solvent mixture is supported. You can pack multiple molecule types, such as a solute and water, into a defined cubic region like a 40x40x40 Å box to create the solvated system for your MD studies.
Packmol is required to pack molecules into a liquid box. This Skill serves as an automated interface for the Packmol engine, requiring it to be installed in your environment to process input coordinates and generate the packed molecular configurations.
PDB and XYZ are the supported input coordinate formats for creating molecular mixtures and layered interfaces. Optional SMILES conversion is also available via Open Babel if you need to generate initial 3D coordinates from chemical identifiers before packing.
Converting SMILES strings into 3D coordinates for packing into mixtures is handled via Open Babel. This optional step generates the initial PDB or XYZ input files required by Packmol to build your specified liquid boxes or solvated systems.
Hello-QMConvert molecular formats and generate 3D coordinates with Open Babel.
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