Computational Chemistry 1.2 - PDB File Format

[@randomwords102]

This is freaking amazing. Thank you so much!

[@TMPChem]

I appreciate this very non-random selection of words.

[@weekendresearcher]

Thanks a ton! Got a pdb of a proposed inhibitor for 2019-nCoV..can study the files better now.

[@rtgo]

Very useful video for starters with the PDB format. Small note: it is B-factor, not Beta-factor.

[@TMPChem]

I looked around quite a bit after your comment to see if there is any source which refers to it as "beta" rather than "b", and I can't seem to find any. Perhaps it is a fabrication of my imagination. I assume the choice of "b" starting with the same letter as the thermodynamic property "beta", or inverse temperature times Boltzmann constant is a non-coincidence, though I'm surprised to see it not referred to as such in any references. Strange.

[@mrhisenberg1763]

How can I change the charge of a metal ion like Zn in a pdb file to perform docking?

[@Gokrix]

Thanks I was searching for this, do you think you can also do a tutorial on using bioPython for PDB?

[@TMPChem]

Hi Gokul. I'm not an expert in many of the tools that are commonly used among macromolecular / atomistic biomodeling researchers. My experience is primarily in gas phase small molecule simulations where structure generation is not a prohibitively complicated problem as it is for proteins / nucleotides / etc. in the absence of good crystal structures. I'm happy to comment where my experience has given me the ability to, but it is wise for individuals to stay in their lane in public while discussing highly specialized topics in the role of an expert / authority figure.

[@devargyachakraborty9068]

@@TMPChem do you have any tutorial of ionic liquid simulation uswing LAAMS

[@joachimjohansen5796]

Thank you so much!

[@TMPChem]

Thanks for watching, Joachim.

[@sabrango]

thx!

[@andreyvartanyan6964]

Thanks u

[@vicenterubio6218]

Drink some water before recording. Avoid the cotton mouth.

[@TMPChem]

Sadly it's pretty much unavoidable. I drink a lot of fluids in daily life and am still clearing my throat all the time.

[@marianaql]

Well done! Thx

[@TMPChem]

Thanks, Mariana!

[@nithya2003]

Thank you so much!!