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

Justin A. Lemkul jalemkul at vt.edu
Thu Oct 15 14:17:59 CEST 2009

Tsjerk Wassenaar wrote:
> 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.

Oops, indeed Tsjerk is quite right.  I thought about that far too quickly (I 
think my brain somehow jumped to the glutathione structure for some unknown 

Defining appropriate connectivity is indeed the problem, but not how I described 
it.  Apologies for the error, and thanks Tsjerk for catching me on it.


> Cheers,
> Tsjerk


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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