Possible upd for SBM course

[AnnaKravchenko]

1. Suggest to bring a mouth for the pymol
2. During the linux session make sure students read about environmental variables, cat, nano (or vim)
3. Encourage students to not be afraid of errors

[AnnaKravchenko]

maxwarn should come with a single ‘-‘, currently there’s two

[AnnaKravchenko]

precalculated results are un-capped, so it is not possible to merge trajectories with student’s capped runs

[AnnaKravchenko]

Aproximate schedule to show on the 1st day
Monday: set up, familiarize with Linux
Tuesday: Homology
Wednesday-Friday: start MD production
Monday-Tuesday: analyze MD run
Wednesday: docking
Thursday: analyse docking results & start report
Friday: report

[AnnaKravchenko]

Ask students to make haddock account on first Monday.
Aks students to request guru on second Monday
(they are sad they have to wait now)

[AnnaKravchenko]

Point to all the plots generated during clustering the trajecories - to help to pick 5 representatives out of all 10-15 clusters

[AnnaKravchenko]

Note:

• sometimes peptide can stretch over the given dimention of a box. In this case, it’s size have to be inceased.
• carefull with disordered part of MDM2 covering the binding side for p53

[AnnaKravchenko]

https://matt.might.net/articles/basic-unix/