CHARMM-GUI Multicomponent Assembler for Modeling and Simulation of Complex Multicomponent Systems.

ABSTRACT: Atomic-scale molecular modeling and simulation are powerful tools for computational biology. However, constructing models with large, densely packed molecules, non-water solvents, or with combinations of multiple biomembranes, polymers, and nanomaterials remains challenging and requires significant time and expertise. Furthermore, existing tools do not support such assemblies under the periodic boundary conditions (PBC) necessary for molecular simulation. Here, we describe Multicomponent Assembler in CHARMM-GUI that automates complex molecular assembly and simulation input preparation under the PBC. We demonstrate its versatility by preparing 6 challenging systems with varying density of large components: (1) solvated proteins, (2) solvated proteins with a pre-equilibrated membrane,

SUBMITTER: Kern NR 

PROVIDER: S-EPMC10491218 | biostudies-literature | 2023 Sep

REPOSITORIES: biostudies-literature