The Program MolDyn is designed to perform multiple tasks with protein structure:
• 1) restoration of missing coordinates of heavy atoms of side chains;
• 2) restoration of missing coordinates of all hydrogen atoms;
• 3) optimization of a protein structure via local energy optimization in an implicit/explicit water solvent;
• 4) optimization of a protein structure via MD simulation in water solvent;
• 5) optimization and folding of a protein via a user defined simulated annealing protocol coupled with force field variation.
• 6) optimization of a user defined flexible protein segments with user defined restraints;
• 7) simulation of the molecular dynamical trajectory of atomic coordinates and potential energy for statistical analysis.

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Description

Parameters

Parameter and Input file description

Test examples description

Docking of Ligand on Protein