MOIL Examples

-- Image files are saved by CMOIL directly --

I. Examples presented on CBSU workshop by Alfredo Cardenas.

1. Solvating the Arc Repressor protein dimer in preparation for simulation starting from its PDB file

1. Use MOIL to read the PDB file (1PAR.pdb), obtain sequence information (poly file), connectivity information (wcon file) and convert from PDB format to moil coordinate file (CRD file);
2. Solvating the protein in a box of water molecules.
image_1 , image_2 , image_3

2. CO diffusion out of myoglobin using conventional MD and Locally Enhanced Sampling (LES) algorithm

1. Create a connectivity file (wcon) from a sequence (poly) file;
2. Use the LES protocol to enhance the sampling of a small part of the molecule;
3. Perform energy minimization;
4. Run molecular dynamics;
5. Analyze the results.

3. Compute a trajectory for folding of an Alanine-rich helix using the SDEL algorithm

1. Use the chmin module and the SPW algorithm to compute a minimum energy path between unfolded and folded structures;
2. Use of SDEL to compute the coil to helix folding (also demo slides).

II. Other Examples:

1. Overlapping two structures with CMOIL:

1D06.pdb & 1DP6.pdb

III. Questions: