Quirks and caveats

Using with GROMACS

1. Take care that the updated residuetypes.dat is present in your working directory
2. Because the greek τ letter can be present in β-amino acids (e.g. N_τ1 and N_τ2 if an arginine side-chain is substituted in the β³ position), they can clash with the NT* and OT* atoms of various C-terminal groups. To resolve this, we have renamed the corresponding terminal atoms to NW* and OW*.
3. If gmx pdb2gmx complains about missing atoms, run it with the -v option, and look for automatic atom renaming (e.g. because of the xlateat.dat file). Sometimes overriding the system-wide atom renaming file in the current working directory can help.

4. Avoid storing molecular geometries of beta-peptides in PDB files for two reasons:

   1. the length of residue names is limited to 3 characters (four is non-standard)
   2. the precision of the coordinates is limited

   The .g96 file format is preferred:

   1. it supports 5 character residue names
   2. can store coordinates (even velocities) in high precision
   3. supports multi-model files as PDB
   4. PyMOL can load it easily
   5. in contrast to its name, gmx pdb2gmx accepts it as an input file