Recently I had some trouble setting up a system consisting of two cysteine residues interlinked via a disulfide bridge. Both residues should be protonated in zwitterionic state. Initially I could not build the topology (OPLS-AA force field) with pdb2gmx. Finally I figured how to do it and I like to share the solution here. Read more »
Eventually I figured out how to paste code snippets into IPython. Actually I found that there are two similar ways to paste your code:
You can either have IPython grab the snippet from your clipboard or you can enter and/or modify it interactively. Read more »