Prepare ABFE and RBFE command workflows for ligand parameterization and simulation setup.
npx skills add https://github.com/Ericwang6/easybfe --skill easybfe-cli
Please help me install this Agent Skill. Skill: easybfe-cli Source: https://github.com/Ericwang6/easybfe/tree/main/skills/easybfe Command: npx skills add https://github.com/Ericwang6/easybfe --skill easybfe-cli
This Skill removes the friction of preparing and analyzing protein-ligand binding free energy workflows, helping you move from raw ligands and a receptor structure to runnable EasyBFE simulation directories and results.
Ask for an EasyBFE workflow that parameterizes my ligands, prepares the ABFE or RBFE configuration from my protein file, and sets up the run directories for analysis.
High-intent search queries and answers about installing and using this skill.
To set up ABFE and RBFE workflows, you can generate simulation directories, config-driven run layouts, and restraint or mapping setups using EasyBFE subcommands for single or batch ligand networks.
Yes, protein-ligand binding free energy simulations support Amber-compatible force fields. You must provide parameterized ligand directories and YAML or JSON configuration files to build the workflow.
The best way to analyze absolute binding free energy results is by running MBAR-based analysis on completed simulation trees to summarize binding free energy outputs consistently.
You prepare a batch ligand network for relative binding free energy calculations by parameterizing ligands into Amber-compatible directories and using the RBFE subcommand to generate mapping setups.
Yes, parameterized ligand directories are required before starting simulation setup. The workflow relies on these pre-parameterized inputs alongside your protein structure to generate runnable directories.
ABFE and RBFE run directory generation supports YAML and JSON configuration files to define the simulation layout and drive the free energy workflow preparation.
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