Bibo Feng

4 Questions 2 Answers 0 Followers

Questions related from Bibo Feng

Assertion Failed error in GROMACS Replica exchange molecular dynamics tutorial ?

I am currently going through the following tutorial for replica exchange MD on gromacs: https://www.gromacs.org/@api/deki/files/209/=tutorial.pdf When I got to stage 2 and tried to create the...

30 January 2022 2,199 3 View

How to use Pymol or VMD to visualize hydrogen bonds between protein and water ONLY (no water-water hydrogen bonding)?

To visualize hydrogen bonds in Pymol between a protein and the surrounding water molecules, I tried using "Action -> Find -> Polar Contacts -> Involving solvents", which shows hydrogen...

15 January 2022 4,292 2 View

Is the protein "structure sculpting" tool no longer available in the newer versions of Schrodinger's Maestro?

I found an old tutorial video from 2013 on Maestro's "Structure Sculpting" tool for building peptides, which seems really useful to me. However, I currently have the 2020 version of Schrodinger,...

31 October 2021 7,408 1 View

Pymol peptide builder errors?

When I tried building the peptide sequence "KEPAPTT" on Pymol, I get the following error after trying to add alanine:...

31 October 2021 5,152 3 View