[gmx-users] Topology for pyroglutamic acid

[Erik Lindahl]

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):
>
>        O
>        "                          CH2-CH2
>    H2N-C-CH2-CH2                  |   |
>              |          --->    O=C   CH-C-...
>          H2N-CH-C-...              \ /   "
>                 "                   N    O
>                 O                   |
>                                     H
>
>
>  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.
>
Hi Lieven,

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?

Cheers,

Erik