We are excited to announce the availability of the AMBER force field in VMD/NAMD, enhancing our ability to prepare and run molecular dynamics (MD) simulations with different force fields. Utilizing the PSFGEN file builder, available as a VMD plugin, one can now apply the AMBER force field natively in VMD 1.9.4 without tedious constraints file formatting. This flexibility allows for the study of large systems that were previously impractical to model with AMBER alone. The integration leverages the strengths of AMBER, renowned for its precision in modeling biomolecular systems, and brings it into the VMD and NAMD environment, known for their ability to run large systems efficiently and for their powerful visualization and analysis capabilities. Researchers can now explore complex biomolecular dynamics with unprecedented accuracy and scale, opening new avenues for groundbreaking discoveries in structural biology. More details about AMBER for NAMD can be found in a recent publication in the Journal of Chemical Information and Modeling.
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- GOLEM: Automated and Robust Cryo-EM-Guided Ligand Docking with Explicit Water Molecules. J. Chem. Inf. Model., 64:5680-5690. 2024.
- Broadening access to small-molecule parameterization with the force field toolkit. J. Chem. Phys., 160:242501. 2024.
- Topological Learning Approach to Characterizing Biological Membranes. J. Chem. Inf. Model., 64:5242-5252. 2024.
- APACE: AlphaFold2 and advanced computing as a service for accelerated discovery in biophysics. PNAS, 121:e2311888121. 2024.
- Improved Highly Mobile Membrane Mimetic Model for Investigating Protein–Cholesterol Interactions. Nat. Commun., 64:4822-4834. 2024.
- A Gram-negative-selective antibiotic that spares the gut microbiome. Nat. Commun., 630:429-436. 2024.
- Beyond nothingness in the formation and functional relevance of voids in polymer films. Nat. Commun., 15:2852. 2024.
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