BioSimSpace Examples

This repository contains example .pdb files that successful pass through tleap ( Ambertools ) providing full input and output for a command line use of tleap. These serve as test cases and examples that can be used for setting up systems with BioSimSpace.

Directory structure:

protein   
  |---input    
        |----input files needed for tleap   
  |---output   
        |---- output generated for tleap

In the input directory contains all necessary information needed for running tleap and the output shows the example output generated by running the input commands. Command line arguments should be place in a file called command.txt and the input input.txt.

Single molecule system examples

All the examples below should consist of a single molecule.

Protein systems

HSP90 (2JJC)
MDM2 (1Z1M)
Thrombin
Cyclophilin A
Lysozyme

DNA/RNA system

DNA Hairpin (1D66)

Other molecules with parameters (other_molecules)

water
lipids
ions
co-factors

Other molecules without parameters (small-molecules)

benzene
FXR_79
cyclosporine
HSP90_82p2
HSP90_82p2-sqmfailure
HSP90_82p7
HSP90_84p1-sqmfailure

Mapping examples (small-molecules at the moment)

benzene-to-chlorobenzene
benzene-to-chlorobenzene-spatiallyclosest
HSP90_82p2-to-HSP90_84p1
FXR_79-to-benzene
FXR_79-to-HSP90_82p2