On Tue, Apr 28, 2015 at 9:51 AM, Robert Molt <rwmolt07.gmail.com> wrote:
> Hello,
>
> The definitions of the terms may be an issue here, for me. You describe
> cc as "non-pure aromatic system." I do not know what that means? In the
> original GAFF paper, it describes it as "inner sp2 carbon on conjugated
> ring systems." I assume that means the fusion points (the "inner" part)
> on these conjugated rings, and hence there have to be exactly two.
>
> Regardless, if the system is sufficiently non-canonical that either
>
> a.) antechamber's specific atom designation subroutine called makes a
> "mistake" in designation
> b.) antechamber's specific atom designation subroutine does NOT make a
> mistake and parameters are missing
>
> then I should perhaps parameterize this on my own.
>
Did you by any chance try to use parmchk2 to "fill-in" the missing
parameters? If not, there's a good chance that parmchk2 will be able to
find some suitable parameters for you.
Also, purine is a rather common biological fragment, so I doubt it lies
outside of the chemical space targeted by antechamber.
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Apr 28 2015 - 07:00:09 PDT
