Force Fields, Parameterization & System Building — Hands-on

Learn how to choose and apply biomolecular force fields, generate parameters for ligands and cofactors, and assemble complete solvated, neutralized systems ready for docking, MD and free-energy simulations. This module focuses on practical, reproducible system-building workflows for proteins, nucleic acids, membranes and small molecules.

Force Fields, Parameterization & System Building

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Session Index

Session 1 — Force Field Concepts & Choices Session 2 — Ligand & Cofactor Parameterization Session 3 — System Assembly, Solvation & Ions Session 4 — Mini Capstone: MD Ready System Build

Session 1

Fee: Rs 8800

Force Field Concepts & Choices

What a biomolecular force field represents and its components

bonded and non bonded terms electrostatics and van der Waals limitations of classical models

Common biomolecular force fields and use cases

AMBER style families CHARMM style families OPLS and other variants

Selecting a force field for proteins, nucleic acids and lipids

compatibility with water models membrane and lipid parameter sets cross compatibility with ligand parameters

Session 2

Fee: Rs 11800

Ligand & Cofactor Parameterization

Preparing small molecules for classical MD force fields

protonation and tautomer states 3D conformer generation overview sanity checks for chemical structure

Charge models and partial charge derivation concepts

AM1 based and RESP style ideas formal vs partial charges consistency with protein force field

Topology generation and parameter sanity checks

bond and angle parameters coverage missing or guessed terms overview basic test minimization of isolated ligand

Session 3

Fee: Rs 14800

System Assembly, Solvation & Ions

Building protein–ligand and complex topologies

combining protein and ligand parameters handling cofactors and metal ions checking connectivity and naming

Simulation box, solvation and water models

box shape and padding distance TIP3P and other water families visual inspection of solvated system

Charge neutralization and ion placement strategies

computing net charge and neutrality adding salt to mimic ionic strength avoiding bad ion placements near sites

Session 4

Fee: Rs 18800

Mini Capstone: MD Ready System Build

Select target, force field family and ligand/cofactors

Theory + Practical

Parameterize small molecules and assemble solvated, ionized box

topology and coordinate generation sanity checks and quick minimization export of MD input configuration

Deliverables: MD ready input set and build report

topology and coordinate files system summary (size, composition, charge) documented build steps for reuse

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Force Fields, Parameterization & System Building Training | Ligand Parameters, Solvation & MD Ready Systems

Force Fields, Parameterization & System Building — Hands-on