[gmx-users] Topology for pyroglutamic acid
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):
H2N-C-CH2-CH2 | |
| ---> O=C CH-C-...
H2N-CH-C-... \ / "
" N 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.
Vrije Universiteit Brussel
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