[gmx-users] Topology for pyroglutamic acid
lindahl at stanford.edu
Mon Jun 3 19:33:32 CEST 2002
Lieven Buts wrote:
> 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.
I have opls-aa working and currently I'm debugging it. I'm pretty sure
there are special types for 4- and 5-member cyclic amines, so I'll see
if I can implement PCA/PGA as a terminus.
Which name is more common, and are there any other similar
rearrangements you need?
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