AMBER Archive (2004)

Subject: Re: AMBER: back interpret

From: David A. Case (case_at_scripps.edu)
Date: Wed Sep 15 2004 - 17:23:18 CDT

On Wed, Sep 15, 2004, Joshua Hicks wrote:

> I'm trying to back interpret some Amber files to get NMR dihedral
> restraints. I've looked at the Amber page at the DNA example, but it
> doesn't help me with the protein files. I've also looked at the Amber 8
> manual, but because we don't have Amber I have no way of testing whether
> or not I'm getting it right. I am trying to calculate PHI angles.
> Here is one residue:
>
> &rst iat= 82, 84, 86, 100, r1=-170.0, r2=-160.0, r3= -80.0, r4=
> -70.0, &end
>
> I do not know what the PHI angle is supposed to be for this residue and
> none of the numbers (82, 84, 86, 100) seem to correlate to any of the
> backbone atom numbers in the pdb file (1XOB).

You have to obtain a pdb file created by Amber to get the atom numbering
used internally in the program. Since all hydrogens are present, etc., this
is almost never the same as the atom numbering in the original PDB file
from RCSB. Furthermore, RCSB reorders atoms within a residue so that the
backbone atoms come first, but Amber does not do this.

The prmtop file also lists the atoms in order, so if you have that, you
could figure out which residue is being referred to. Easier would be
to run ambpdb to get an pdb with the Amber numbering. The person who provided
the constraint file (quoted above) should also have these other files as well.

(Assuming this came from a real person, and not from PDB supplementary
material or the like. If it's the latter, and you send me details, I can
probably figure out how to reproduce the files that are used. 1XOB is one
of "my" structures [from a decade ago....] so I'm sure we can get this figured
out.)

...dac

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