CHARMM-GUI KIAS School

 

September 23 - 25, 2019         Rm8101 of Buld.8, KIAS, Seoul

Program Home > Program

Day 1 (September 23)

 

< morning lecture: 9:00 - 12:00>

  • 9:00 - 9:50 Molecular mechanics & force field (Jeff  Kladua)

  • 10:00 - 10:50 Minimization & molecular dynamics (Jeff Kladua)

  • 11:00 - 11:50 CHARMM-GUI Lectures & common errors (Jumin Lee / Wonpil Im)

 

 

  • Introduction of participants (1-2 slides) 

  • PDB Reader & Manipulator for reading PDB and PDBx/mmCIF structure files and modifying side chains (e.g., mutation, phosphorylation, protonation, heme coordination, lipid-tail linkers, GPI-linker, glycosylation, spin labels, fluorophores, and unnatural amino acids) 

  • Glycan Reader & Modeler for preparation of simulation systems containing carbohydrates or glycoproteins

  • Ligand Reader & Modeler for generation of force field (FF) for ligands

  • Glycolipid and LPS Modeler for generation of various glycolipid and lipopolysaccharide structures 

  • Nanomaterial Modeler and Polymer Builder for generation of various nanomaterials and polymer systems

 

 

 

Day 2 (September 24)  

 

< morning lecture: 9:00 - 12:00>

  • 9:00 - 9:50 Lipid membrane simulations (Jeff Kladua)

  • 10:00 - 10:50 Martini force field (Siewert-Jan)

  • 11:00 - 11:50 HMMM, PACE force field, MDFF/xMDFF (Yifei Qi)

 

 

  • 1:00 - 1:50 Enhanced sampling & free energy simulation (Yuji Sugita)

  • Solution Builder for solution simulation system generation. 

  • Membrane Builder for generation of bilayer, monolayer, micelle, nanodisc, hexagonal lipid phase, and vesicle systems with and without proteins

  • HMMM Builder for building membrane systems using the highly mobile membrane mimetic (HMMM) model

  • PACE CG Builder and Martini Maker for coarse-grained simulations using the PACE FF and the Martini FF

 

 

 

Day 3 (September 25) 

 

< morning lecture: 9:00 - 11:25>

  • 9:00 - 9:50 Advanced sampling techniques and free energy simulation (Bernie Brooks)

  • 10:00 - 10:25 Ligand Binder (Seonghoon Kim) 

  • 10:25 - 10:50 Multicomponent Assembler (Nathan Kern)

  • 11:00 - 11:25 Programing with CHARMM-GUI (Sunhwan Jo)

 

 

  • Ligand Binder for free energy perturbation MD simulations for protein-ligand binding affinity calculations

  • Multicomponent Assembler in solution and membrane

  • PBEQ-Solver for electrostatic potential online visualization. 

  • MDFF/xMDFF Utilizer for MDFF/xMDFF Utilizer for setting up molecular dynamics flexible fitting (MDFF) simulation system inputs using electron density maps and low resolution crystallographic data as restraints

  • Presentations from participants