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
reason...)
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.
-Justin
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
