GROMACS version: 2021
GROMACS modification: No
I need to create some stapled peptides. I can fairly easily pull the parts I need from charmm36 merged ff file. But I seem to have two choices. I can create a ‘double’ residue, with two latent amide bonds and two entries for cmap, or according to an online source, I could define a link in specbond. I cannot find any details on how to use specbond (if that is the correct method). In particular though, it is not clear how to break the link into two residues. The staple I need is a cis alkene in the middle. Should I create two asymetric residues, one with a terminal double bond and separately labelled terminal protons and a second shorter residue with specbond saying how to link? I suppose I could hunt through source for how specbond is used, but I’d much appreciate any pointers here if possible.
Here is the information from the manual about specbond.dat:
Thank you! In hindsight I don’t know why I couldn’t find it but I had tried searching the documentation for specbond and that didn’t come up.