HMMer notes, avoid redundant searching

PyMol notes, avoid redundant searching

Visualize Amber nc trajectory in PyMol
I used to convert everything into .dcd file but it is a little complex. Now I found PyMol actually can directly read prmtop & nc file but just need little adjustment.

VSCode notes, avoid redundant searching

Reference:

GitHub repo from the developer (https://zimmermangroup.github.io/pyGSM/)

Personal notes on using pyGSM.

Docking is one of the key problem bringing the substrate to the enzyme modeling. But most current docking methods performs poorly with larger substrates. This note record usages of the AutoDock Vina for testing.

Plot IGM analysis from Multiwfn using PyMol. IGM is an useful analysis of spatial distribution of steric hindrance. Plotting IGM result is much easier and looks better in PyMol.

Related Multiwfn Documents
http://sobereva.com/407

Related PyMol Documents
https://pymolwiki.org/index.php/Ramp_New

Note for using WFRT/NRT methods. Analyze contribution of resonance structures. Understand different seperations of fragmental contribution to the structure.

Note for using CASSCF methods.