Dear Jason, dear Bud,
>> 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.
Yes for all...
Once a first connection is done between two units (using the
"sequence" command), one can also define a new head or a new tail in
this new "two-unit".
You can find many examples of such an approach in R.E.DD.B. for
branched molecules... See for instance:
http://q4md-forcefieldtools.org/REDDB/projects/F-87/
http://q4md-forcefieldtools.org/REDDB/projects/F-87/script1.ff
GLYCAM developer also use this approach to build branched
oligo/polysaccharides...
regards, Francois
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Received on Mon Nov 21 2011 - 00:30:03 PST
