Preparation of Protein system from initial pdb file.

Setup, solvate, equilibrate and analyze

Example system: Snake venom peptide from Green Mamba Snake

Eastern Green Mambas are found in Africa. This tree dwelling snake can grow to eight feet.
The venom is a neurotoxin .

1fsc.pdb structure representation showing disulfide bonds.

Ball-and-stick representation of the 61 amino acids.

• Initial decisions and analysis  (N.B. Read the pdb file carefully)
• Titratable groups
• Xray waters
• Missing residues
• bound ions and coordination complexes
• Unknown ligands and odd residues
• Minimization and solvation < General script
• Put in patches for protein and ligands and any additional rtf and parameter information all into the solvation script.
• Decide on periodic boundary conditions: image or crystal, cubic or octahedral
• venom example modified script with one patch
•  Running the script
•  Equilibrate
• minimize solvent with solute fixed to relieve bad solvent vdW contacts
• In several steps release constraints on the solute in minimization
• Run several ps CPT MD at 300K with weak constraints on the solute
• Run several hundred ps  CPT MD to equilibrate all.
• Analyze energy
• Analyze pressure and temperature
• Density ftp ftp.scripps.edu << EEEOF
• RMSD
• Atomic Fluctuations
• Trajectory Analysis
• Atomic Fluctuations
• rmsd time series
• Energy, temperature, density time series
• P2 correlation functions and order parameters