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Ren lab, The Department of BioMedical Engineering, The University of Texas at Austin

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Contents 1 AMOEBA Parameterization 1.1 CLICK HERE Poltype - Atom typer for the AMOEBA polarizable force field 2 AMOEBA in AMBER 3 AMOEBA in TINKER

AMOEBA Parameterization

CLICK HERE Poltype - Atom typer for the AMOEBA polarizable force field

• More on AMOEBA Parameterization
• A tutorial on how to manually obtain multipole paramters

AMOEBA in AMBER

• click here
• Only work with tinker parameters in v 4.x format (conversion tool available below)
• How to run sander or pmemd with AMOEBA
• Tutorial on binding free energy
• Source code mdofications to incoporate soft-core vdw and ionic damping coefficents
• Hydration free energy calcualtion automation

AMOEBA in TINKER

Changes in AMOEBA parameter format from tinker v 4.x to 5.x