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

From: David A. Case <>
Date: Mon, 16 Jul 2007 17:13:45 -0700

On Mon, Jul 16, 2007, Narayanan Veeraraghavan wrote:

> 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?

This is a known bug of LEaP: basically, the "rule" is: if you modify
(in a frcmod file) one of the multiplicities in a torsion, you need to modify
all of them. Same idea for specific vs. non-specific: if you put in specific
parameters for a torsion, you should include specific versions for all
multiplicites (even those that might have a zero force constant). Basically,
don't leave LEaP any choice about which set (general, specific, frcmod) of
parameters to use.

I think the peptide/protein force fields have been examined for their
compliance with this "rule", but the same might well not be true for sugars.
I've lost track of which force fields you are using, (or even what kind of
molecule.) For now, the "fix" is to make the parameter files more complete,
so that the sort of ambiguity referred to above does not enter.

As we transition from sleap to tleap, Wei should try to see if we can get
sleap to follow well-defined rules for this sort of a situation. Some one
could also earn gold-stars by taking the time to really figure out what tleap
does and why, but I'm not holding my breath.


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Received on Wed Jul 18 2007 - 06:07:35 PDT
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