AMBER Archive (2004)

Subject: Re: AMBER: Improper dihedral

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Mon Jan 12 2004 - 13:23:44 CST

> Sorry, it's that I have it and I used it but forgot to present it in the
> previous message. But here it is, my leap.in file (Obs.: dmacaz.dat is
> my frcmod file):
>
> loadamberparams dmacaz.dat
> y = loadpdb dmacaz.pdb
> set y.DMA.C1 type q1
> set y.DMA.C2 type q2
 ...

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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