On Sun, Nov 20, 2011 at 11:59 AM, M. L. Dodson <mldodson.comcast.net> wrote:
>
> I would appreciate expansion to a broader specification to allow this
> case. But maybe it is already there, and I misunderstood the
> documentation.
>
I think they basically copied the OFF file's approach completely here. The
documentation on their website suggests 2 additional groups. The first
being the definition of the HEAD/TAIL, and the second being the definition
of RESIDUECONNECT, which (like the OFF) allows you to specify up to 6
connect atoms, so I think this feature already exists (Francois can correct
me if otherwise).
In any event, the formation of a cystine (from cysteines) inside a protein
requires the definition of a HEAD, TAIL, and a third connect atom for the
disulfide bond, so a simple head-tail definition doesn't even work for many
pure proteins.
That being said, I don't know how much leap actually uses the connection
sections of the OFF file anyway (outside of creating head-tail and
tail-head bonds). The "bond" command is needed in tleap to create
disulfide bonds despite the 6-way connect sections of the OFF file.
All the best,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Nov 20 2011 - 13:00:04 PST
