Re: AMBER: back interpret

From: Carlos Simmerling <carlos.ilion.bio.sunysb.edu>
Date: Wed, 15 Sep 2004 18:08:40 -0400

the iat numbers are indeed the atom numbers for the restraint.
amber will renumber atoms, so looking at the pdb file numbers
won't necessarily match.
it's a flatwell potential, with no penalty between r2 and r3, and harmonic
between r1 and r2, and between r3 and r4.


Joshua Hicks wrote:

> Hello,
> 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).
>
> Thank you for any help.
>
> Regards, Josh
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Received on Wed Sep 15 2004 - 23:53:01 PDT
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