On Mon, Oct 3, 2011 at 7:57 PM, Peter Eastman <peastman.stanford.edu> wrote:
> There are some atoms listed in nucleic10.lib that specify the atomic number
> as being -1:
>
> "C8" "C5" 0 1 131072 14 -1 0.200600
>
Yep, I see it. The problem is that C4, CS, and C5 were never defined atom
types in ff10.in.
>
> This is true for some bases, but not all of them. What does this mean? Is
> it a bug,
No, It's a feature. :)
> or is there some significance to it? (The documentation doesn't mention
> any possibility of atomic numbers being negative.)
>
I believe no. I can't think of anywhere that the atomic number or element
are actually used (the only things that matter are the bits and pieces that
go into the equations, namely the VDW parameters, charge, mass, etc. The
force field couldn't care less about protons vs. neutrons).
To the Amber decisionmakers -- does this warrant a bugfix? I've fixed it in
the main branch, but should it be turned into bugfix.next?
HTH,
Jason
> Peter
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Oct 03 2011 - 20:00:03 PDT
