Re: [AMBER-Developers] AT Manual feedback request

--
Yong Duan, Ph.D, Professor
UC Davis Genome Center and
Department of Biomedical Engineering
University of California at Davis
Davis, CA 95616
530-754-7632
On 11/27/11 12:43 PM, "B. Lachele Foley" <lfoley.uga.edu> wrote:
>>What I meant by "improper" was that the order of the atoms can imply an
>> improper torsion. I think (.N:3-.C:3-.CA:3-.CB:3) is actually an
>>improper
>> torsion (CA connects to all three other atoms). But, I think Dave meant
>> .N:4-.C:3-.CA:3-.CB:3 instead, which is a proper torsion, is actually
>>the
>> PSI' torsion. The difference is just .N:4 vs .N:3.
>
>I didn't do comprehensive testing yet, but from what I observed so far,
>let's say you specify
>
>impose m {4} {A B C D 30.0}
>
>Leap goes to residue 4 and finds an atom called "A".  It then looks for
>an atom called "B" that is bonded to A without regard to the identity of
>the residue that contains B.  If it doesn't find a bonded atom, B, it
>stops.  If it finds one, it looks for C bonded to B and D bonded to C in
>the same manner.  Then, it applies the torsion around the B-C bond.  So,
>it wouldn't act on an improper torsion because at some point it won't
>find a bond.
>
>:-) Lachele
>
>Dr. B. Lachele Foley
>Complex Carbohydrate Research Center
>The University of Georgia
>Athens, GA USA
>lfoley.uga.edu
>http://glycam.ccrc.uga.edu
>
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