AMBER Archive (2009)

Subject: Re: [AMBER] question with pucker in six member ring

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Mon Oct 19 2009 - 12:54:03 CDT

> Thanks Bill. I ran the carnal with analin. A question comes as in the output is
> L0 4.670143e-02 2.188132e+02 1.754455e-02
> L0 3.509093e-02 2.200238e+02 3.836253e-02
> L0 6.396239e-02 3.068664e+02 5.300770e-03
> L0 1.539782e-01 2.853569e+02 3.012650e-03
> L0 1.104845e-01 2.803663e+02 -3.327869e-03
> L0 9.261769e-02 2.268125e+02 -8.909780e-02
> L0 8.826193e-02 2.053027e+02 -8.114358e-02
>
> Does this mean amplitude puckerangle and then what is the third column.
> A second question is in the analin input file does it matter what
> order I give to the atoms for whom the pucker needs to be
> calculated.

You would have to read the paper that is referenced. It has been a while
since I wrote the code, and I've largely forgotten about it now. But the
output is probably always the number of ring atoms - 3.

Bill

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber