[gmx-users] Re: Re: Pyroglutamic Acid - Topology (pdb2gmx)

[Tsjerk Wassenaar]

Hey,

> The problem comes from the special linkage between PGL and whatever the
> subsequent amino acid is - the amide is formed through the side chain.  As
> such, you will need to specify a special bond in specbond.dat before this
> connectivity will be recognized.  If this is successful, then the PHE should
> no longer be recognized as a terminal residue and thus will not receive any
> additional protonation.

That's not correct. Pyroglutamic acid is basically a proline with an
oxy group due to formation of an intra-residue ester bond. There's no
bond between the side chain and the next amino acid.

Cheers,

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623