Universiti Sains Malaysia

1
Universiti Sains Malaysia
Ranmali Perera

July 18, 2008
Comparison of AutoDock and GAMESS/APBS Methods
for Performing Molecular Computations on
Biological Systems
2
Proposed Research

• The enhancement of previously designed framework
  for ligand-protein investigations using
  GAMESS/APBS tools
• Comparison of data obtained from AutoDock and
  GAMESS/APBS
• Visualization, analysis, and archival of results
• NIMROD will be used for this workflow

3
Progress

• Manually created GAMESS output files for the 20
  smallest ligands from the NCI Diversity Set
• Obtained accounts for the Zurich, UCSD, and
  Monash Nimrod portals
• Attempted to run GAMESS using command lines as
  well as the Zurich Nimrod portal
• Ran the APBS script Celine sent
• Tried to run GAMESS using the Monash Nimrod
  portal
• Obtained a protein to use for APBS and AutoDock

4
Goals for the Future

• Do further research on the protein (HDM2) and the
  beta-hairpin (inhibitor of HDM2)
• Run GAMESS and APBS using Nimrod for 100 ligands
• Run AutoDock manually
• Run AutoDock with GridSphere for the entire NCI
  Diversity Set

5
Achievements

• Running GAMESS manually for 20 ligands on one CPU
• Running APBS manually for HDM2 and the
  beta-hairpin on one CPU
• Gaining access to four nodes in lab, which allows
  me to run GAMESS and APBS in a faster, more
  efficient way
• Obtaining accounts on the Zurich, UCSD, and
  Monash Nimrod portals and finding where GAMESS
  and APBS are installed

6
Major Problems

• Solution
• Talked to Dr. Habibah and Wai Keat about how many
  ligands I should use decided to try to use at
  least 50, ideally 100 ligands.
• Skyped with Dr. Abramson and asked my questions
  about Nimrod.
• Asked Celine about how to go about doing this.
  She sent a script (gam2pqr), but this does not
  work either. Im currently trying to find an
  alternative.

• Problem
• Time realistically, how many ligands can I use
  for both methods?
• Using Nimrod running experiments and adding
  resources
• Converting GAMESS output files (for the NCI
  Diversity Set ligands) to pqr files

7
The legend of Mahsuri (Langkawi Island)
Two men wearing the traditional Malay Baju Melayu
(outfit) and Songkok (cap)
One of the many monkeys at the Botanical Gardens
At the Botanical Gardens
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Talking to the children at the village
Group picture!
A huge pile of durian at a night market in
Langkawi
Peters visit to Malaysia