This sounds like it could be a bug. I don't recall all the ins and
outs of the dihedral term application in leap so whoever is responsible
for it now should respond.
Bill
> I once again looked into this issue of specific and generic dihedrals.
> It seems that in some instances tLeap choses to include both generic
> and specific dihedrals (with different multiplicities) whereas in
> other instances it simply ignores the generic dihedrals (even when the
> multiplicities are different).
>
> For example:
> H2'1 - C2' - C3' - O3' 0.250 0 1 (H1-CT-CT-OS)
> H3' - C3' - C2' - O2' 0.250 0 1 (H1-CT-CT-OH)
>
> The above, have just the specific dihedral entry in the topology, but
> not a non-specific inspite of the fact that the generic dihedral
> X-CT-CT-X has a multiplicity of 3.
>
> Cases where AMber includes non-specifics
> H4' - C4' - C3' - O3' 0.156 0 3 (H1-CT-CT-OS - non specific)
> H4' - C4' - C3' - O3' 0.25 0 1 (H1-CT-CT-OS - specific)
>
> H5'1 - C5' - C4' - O4' 0.156 0 3 (H1-CT-CT-OS - non specific)
> H5'1 - C5' - C4'_O4' 0.25 0 1 (H1-CT-CT-OS - specific)
>
> Could someone kindly tell me if I am missing something?
>
> Thanks,
> Narayanan
>
> On 7/9/07, Bill Ross <ross.cgl.ucsf.edu> wrote:
> > I believe the multiplicity must also match for a specific dihedral
> > term to replace a general one, e.g.
> >
> > Again for H4' C4' C3' O3' (atom types: H1 CT CT OS)
> > 34: 0.250 0.00 1.0 H4' C4' C3' O3' (9,8,25,31)
> > 35: 0.156 0.00 3.0 H4' C4' C3' O3' (9,8,25,31)
> >
> > The multiplicity of 1.0 comes from the specific term, the one
> > for 3.0 comes from the general term (X-CT-CT-X).
> >
> > Bill
> > -----------------------------------------------------------------------
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Received on Wed Jul 18 2007 - 06:07:34 PDT
