Perform a Molecular Dynamics Simulation in Solution.
A 3D structure that you’ve previously generated on Glycam-Web is subjected to an energy minimization and molecular dynamics simulation to generate a trajectory of shapes that it adopts in solution.
Overview
Currently in alpha testing. User accounts will be approved for beta testing soon. This tool allows you to perform an MD simulation with structures you’ve generated on Glycam-Web. The simulation is performed using Amber, and all the details are made available in the output file. You will be able to download the resulting trajectory for your own analysis.
Requirements
- A user account on Glycam-Web that has been approved for alpha-testing.
- A previously 3D structure generated on Glycam-Web that is associated with your user.
Actions
An account is required for tracking projects. If you don't already have an account, you will need to register, then return to this page.
Assemble a glycan by connecting monosaccharides. This is the legacy tool.
Assemble a glycan by connecting monosaccharides. This new tool is still in development.
If you didn't send your project to the MD tool in the Carbohydrate Builder, you can still do it in your project detail page.
Learn More
Citations
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1. C.Tian, K. Kasavajhala, K. A. A. Belfon, L. Raguette, H. Huang, A. N. Migues J. Bickel, Y. Wang, J. Pincay, Q. Wu and C. Simmerling., "ff19SB: Amino-Acid-Specific Protein Backbone Paramters Trained against Quantum Mechanics Energy Surfaces in Solution." J. Chem. Theory Comput.16. (2019) 528-552
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2. Roe DR, Brooks BR, A protocol for preparing explicitly solvated systems for stable molecular dynamics simulations. J Chem Phys.. (2020 Aug 7) 153
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3. R. Salomon-Ferrer, A.W. Goetz, D. Poole; S. Le Grand, and R.C. Walker, "Routine microsecond molecular dynamics simulations with AMBER on GPUs. 2. Explicit solvent Particle Mesh Ewald." J. Chem. Theory Comput.. (2013) 9, 3878-3888
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4. Kirschner KN, Yongye AB, Tschampel SM, González-Outeiriño J, Daniels CR, Foley BL, Woods RJ, GLYCAM06: a generalizable biomolecular force field. Carbohydrates. J Comput Chem.. (2008 Mar;29) (4):622-55