[gmx-users] Topology for pyroglutamic acid

Lieven Buts lieven at ultr.vub.ac.be
Mon Jun 3 17:06:36 CEST 2002

  In one of the proteins I am looking at the N-terminal
glutamine residue has undergone cyclisation to pyrrolidone
carboxylic acid (PCA), also known as pyroglutamate (PGA):

        "                          CH2-CH2
    H2N-C-CH2-CH2                  |   |
              |          --->    O=C   CH-C-...
          H2N-CH-C-...              \ /   "
                 "                   N    O
                 O                   |

  According to Creighton, this is a common rearrangement
for N-terminal glutamines.

  For the time being I am using an unmodified glutamine
for my GROMACS model, and I don't think this difference
is very important in the overall picture, but I was wondering
about the best way to represent this in GROMACS.

Lieven Buts
Vrije Universiteit Brussel

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