On Mon, Apr 29, 2013, sandeep singh wrote:
>
> There is a bug in impose command in amber tleap
This doesn't look to me like a bug, but rather an example of an easily-made
error in setting up the input. Please read carefully the discussion about the
impose command in section 4.5.21 of the AmberTools13 Reference Manual (or
similar section in earlier versions).
If you say this:
impose unit { 3 } { "C" "N" "CA" "C" -154.9 }
this will set the phi torsion of residue *4* to be -154.9: the seqlist value
of "3" says start the torsion at the C atom of residue 3; by conventional
nomenclature, the torsion that will be set will be that of residue 4. If I'm
reading your blog correctly, this is what has happened.
As you point out, one can of course write scripts that make it easier to
specify common torsion angles like phi.
...dac
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Received on Mon Apr 29 2013 - 12:00:03 PDT
