AndyForesterWhatIveDone
HBDI Calculations
- Ran HBDI calculations at B3LYP 6-31G(d) and HF 6-31G(d) levels both OPT and FREQ
- Compared FREQ results to the literature values by A.Esposito et al. - Good agreement.
Comparison to Jasper Von Thor's HBDI calculations
- Not directly comparable since he never published his results on pure HBDI
- He had a larger system with other residues frozen around the HBDI molecule.
- He also used a solvent model
Looked at GFP structures
- 1GFL - Yang et al. -http://www.pdb.org/pdb/explore/explore.do?structureId=1GFL
- 1W7S - Jaspers stucture - http://www.pdb.org/pdb/explore/explore.do?structureId=1W7S
- Chose 1W7S since it was Jasper Von Thor's structure.
1W7S
- Worked how to load without water
- Worked how to load with correct protonation, then corrected chromophore
- Try to run an AMBER OPT - MM parameters missing
- Froze coordinates and wildcards to 0.0
- Errors all around the chromophore
TINKER
- Looked at TINKER for structure minimisation
- Also might be better at parsing the .pdb files
- Issues with .xyz to .pdb conversions
- Turned out to be protonations which differed
- Too much hassle to sort this so early on - MAYBE COME BACK
Protonation of GFP
- Obviously pH conditions will determine protonation of the GFP
- How to determine protonation - Andrew Miller suggets pKa of each residue.
- Easy to change in Gaussview residue editor
- Based on A. Millers advice and accompanying assumptions - protonated at different pH's (5,7,9)
- Not a huge difference in protonation
- based on AMBER charges (sum of residue charges) the overall charge at pH 7 is -6
Running a GFP (1W7S) input
- Used 1W7S with no water and cleaned chromophore
- Doesn't run due to paramters missing
- Freeze and set paramters to 0
- Runs energy calculation
- Charge issues
Computational practical issues
Charges
- Can be calculated via Qeq, ESP, etc...
- Can be AMBER94 assigned in Gaussview atom editor
- Must be integer and sum to the correct overall charge
Testing Charges on mini Biomolecule
- HBDI bridged with a protein bridge (AMBER parameters will fit)
- Calculated with Pure QM and also with ONIOM QM/MM
- With Mechanical Embedding and Electronic Embedding
- Observed energy differences and FREQ differences between them