On Fri, Jun 1, 2012 at 1:01 PM, Marc van der Kamp
<marcvanderkamp.gmail.com>wrote:
> Dear all,
>
> I want to have a protonated glutamine residue (GLH) at the C-terminus, but
> it turns out that GLH is not defined in (any of the)
> $AMBERHOME/dat/leap/prep/aminoct*.in files.
>
This doesn't surprise me. GLH is a funky residue IMO. You have 2
carboxylates in close proximity to one another (the side chain and the
C-terminus), why would you only protonate one of them? Why the side-chain
one? I can't imagine any ensemble that is properly characterized by a
C-terminal glutamate in which the terminus is predominantly deprotonated
and the side chain is predominantly protonated...
This is probably worth considering.
>
> Two questions:
> 1) Has anyone developed parameters (i.e. charges) for this consistent with
> ff99SB or ff12SB?
>
The parameters should be present.
> 2) If not, would a 'simple' solution, in which I'd just add the atoms in
> analogy to GLU and then manually change the charges similarly to the
> changes between GLU in amino12.in and aminoct12.in, be OK? Or would
> redeveloping the charges (e.g. with RED) be the only appropriate solution?
>
My approach (and others may disagree here) is that if the changes you would
make by hand are fairly small, there's probably not much need to re-derive
charges. If the charge differences are large, then rederiving may be an
appropriate option, although you'll have to take care to apply
'appropriate' charge constraints for consistency. (hopefully hand-editing
will work).
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Jun 01 2012 - 10:30:03 PDT
