A few months ago, I finally got around to installing & learning NAMD for doing some molecular dynamics. Installation was (and has been) relatively easy. Leaning how to use it in the past was always a bit too much for me for some reason or another. However, at the encouragement1 of a new postdoc in one of the adjoining labs at work, I gave it another stab with much better results!
So, in a slight change of events, instead of the typical personal blog posts I’ve been doing lately, I feel a need to make a more technical one. Either for others’ benefit or for my own, in the event I happen to lose said notes on how to do this stuff. In any case, these are the summation of online searches, trial & error, and a bit of ingenuity in other random spots, all directed towards the generation, editing, and mapping of surface electrostatics maps on structural models of crystallized proteins. I’ll drop in cited links when I can, pending whether or not I can track some of them down again!