People who run molecular simulations quickly become familiar with all of the things about a PDB file – missing residues, missing heavy atoms in residues, missing hydrogens, non-standard amino acids, multiple conformations, crystallization ligands, etc. – that might need to be fixed before setting up a simulation. This blog post is a reminder to check, after you have “fixed” your PDB, if you have accidentally introduced aberrant cis peptide bonds into your structure during rebuilding.

The vast majority of peptide bonds are trans, with a small fraction (mostly involving proline) in the cis conformation. However, programs like pdbfixer and even the topology rebuilding function of CHARMM (in my case, CHARMM35) will sometimes introduce cis peptide bonds into rebuilt systems. These programs are typically just dropping in a residue template, and sometimes it fails. You can read a detailed discussion of this in the context of pdbfixer here.

Luckily, you can find and fix cis peptides in your structures using the handy VMD tool cispeptide. Once you load a structure into VMD, cispeptide will first find the cis peptide bond and then allow you to select a specific peptide bond atom to flip.

In most cases, just flipping e.g. the “N” atom so that the peptide bond is now trans but the rest of the protein’s configuration has not been altered will result in the “fixed” peptide bond rapidly flipping back to a cis conformation due to the poor local geometry (which is why the rebuilding program had trouble in the first place!). The cispeptide plugin can automatically generate restraints to maintain new trans peptide bonds for NAMD. If you are running in OpenMM like me, you can use a CustomTorsionForce to add a restraint to peptide bond during initial minimization and heating of your system.