PACEff Builder: An Efficient Platform for Constructing PACE Hybrid-Resolution Models for Molecular Dynamics Simulations of Aqueous Protein, Peptide Assembly, and Membrane Protein Systems

Hybrid resolution molecular dynamics offers a practical balance between the accuracy of all-atom models and the efficiency of coarse-grained (CG) approaches. We previously developed Protein in Atomistic details coupled with CG Environment (PACE), a force field that uses a united atom description for proteins and a MARTINI CG environment for lipids, water, and ions. PACE has been validated for native-state stability, ab initio folding of small proteins, peptide self-assembly, and membrane protein applications. However, deployment can be difficult due to variant selection and system-specific construction protocols. Here, we present PACEff Builder, a free web platform that automates PACE model preparation for four common scenarios: aqueous proteins, peptide assemblies, membrane proteins, and mixed-resolution systems that couple PACE protein domains to MARTINI surroundings. The platform provides a unified workflow for structure intake and system parametrization, offers options for terminal capping, lipid composition, ionic conditions, and OPM-based orientation, and generates GROMACS-ready topologies, parameters, and coordinates. To further lower the entry barrier, it pairs a lightweight language model with a deterministic parser that converts natural language requests into complete build configurations. The PACEff Builder streamlines PACE model preparation while maintaining transparency and consistency. The platform is available at https://paceff.com.