AMBER Archive (2004)

Subject: Re: AMBER: Improper dihedral

From: Herbert Georg (hcgeorg_at_if.usp.br)
Date: Mon Jan 12 2004 - 13:39:12 CST

In this case the bonds are recognized as I can see with the desc
command and xleap shows the bonds between the atoms. The centers are in
the 3rd place also. So I don't know why it doesn't apply the impropers.
I suppose that, being the center atom in the 3rd place, it doesn't
matter the order of the remaining 3 atoms, as it seems not to matter in
the case of BONDS and ANGLES.

>How do you set bonds? (As far as I remember, leap ignores CONECT
>in pdb files). If there are no bonds, no impropers will be applied.
>Have you looked at the residue in xleap? See the biotin demo for an
>example of residue-building from pdb:
>
> http://amber.scripps.edu/tutorial/streptavidin/biotin_res2.html
>
>Assuming there are bonds, the next thing to do would be to list
>the impropers you expect to see, then check that the central
>atom of the improper is in the right place (3rd I believe).
>
>Bill Ross
>
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