AMBER Archive (2007)

Subject: Re: AMBER: Specific/Non-specific dihedral issue in Amber

From: Narayanan Veeraraghavan (narayanan.veeraraghavan_at_gmail.com)
Date: Mon Jul 16 2007 - 16:35:53 CDT

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_at_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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