From: Brian Radak (
Date: Tue Apr 10 2018 - 08:58:47 CDT

The user guide is unfortunately lacking in good examples for this.

I have a simple, complete peptide structure for (ALA)_5 and want to make a
new PSF/PDB with psfgen after converting the central residue (resid 3) to
ASP. The mutate command sounds perfect for this. I did something like the

segment PROA {
  pdb foo.pdb
  mutate 3 ASP
coordpdb foo.pdb PROA

which works, but predictably has trouble reading the PDB since it finds the
atom HB3 in ALA when it is expecting CG, etc. from ASP. The guessed
coordinates for the added carboxylate are fairly atrocious with a
completely unphysical dihedral. Is this an expected limitation of mutate?

Obviously it is a bit too much to ask that mutate immediately figure out
the mapping between those two atoms on-the-fly. I was able to tell psfgen
about that mapping by adding:

pdbalias atom ALA HB3 CG

before reading coordinates, but I'm pretty sure this is a global mapping
that discards the HB3 coordinates for all other ALA residues (not what I
want). This works out just fine in my case, but seems unsatisfying as the
solution to the problem in general. Is there a more specific workaround
than this? What would I do for a more complicated mutation like LYS to TYR?