Galaxy |

Convert Parameters (version 21.10+galaxy0)

Input format:

Input topology (prmtop) file:

Ligand selection:

Define a valid AMBER stripmask that will select only the ligand

Receptor selection:

Define a valid AMBER stripmask that will select only the receptor

Complex selection:

Define a valid AMBER stripmask that will select the complex (receptor with ligand)

Solvated complex selection:

Define a valid AMBER stripmask that will select the solvated complex (includes water and ions)

What it does

This tool converts parameter and topology files that represent a solvated complex into parameter files for the ligand, receptor, complex and solvated complex in AMBER prmtop format. These files are needed for MMGBSA/MMPBSA calculations.

How it works

AmberTools' ParmEd is used to strip unneeded atoms and save the parameter files. The stripmasks are defined by the user.

Outputs created

prmtop files for the ligand, receptor, complex and solvated complex.

User guide and documentation

The AmberTools Manual

The Parmed Documentation