Week2 Jan22 Jan28 - WangXueqing007/Master_Thesis GitHub Wiki

Jan 22:

• Today:

  • Solved the "All ATOM and HETATM records must be given before any nested BRANCHes" problem; turns out to be an inadequate preparation in of the receptor.pdbqt file?
  • Group meeting, Marie&Annie's talk.
  • Proceed to exercise 10 in the ADT tutorial.

Jan 25:

• Problem encountered:

  • Choosing a grid--based on what ground?
  • If increasing the grid size by adding the space between points--will that work?

• Sarah's advice:

  • Adjust the trajectory of receptor instead.
  • Leave the flexible residues part aside.

Jan 28:

• Today:
  Learnt a bit about Chimera turn function, explored into BILD format.
• To-do list:

  • GitHub diary editing: less priority. Focus more on actual work but keep track on repository wiki--as important!
  • Urgent: figure out how to adjust receptor trajectory--no matter in VMD or Chimera!
  • Urgent: Learn to use command line! (learn about the environmental variant--less urgent)
  • Not that urgent: figure out how to split the ligand and the receptor from a co-crystallization PDB file.
  • A bit urgent: learn to use Endnote!!!
  • Keep writing your Introduction! --Write when you read!!!!