AMBER Archive (2009)

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

From: Thomas Cheatham III (tec3_at_utah.edu)
Date: Fri Oct 16 2009 - 13:23:05 CDT

> I am trying to calculate the pucker in a six member ring. I use this lines
> in ptraj
>
> trajin data-0.00.crd
> pucker name1 :233_at_C6 :233_at_C7 :233_at_N8 :233_at_C8A :233_at_C4A :233_at_N5 out
> puckerDHPpseudo.dat cremer offset -90.0
> pucker name2 :233_at_C6 :233_at_C7 :233_at_N8 :233_at_C8A :233_at_C4A :233_at_N5 out
> puckerDHPamp.dat cremer amplitude offset -90.0
...
> Could some please help me understand this. thanks, ganesh

This will be meaningless since the pucker command is only currently built
for 5 member rings (only 5 masks of atoms are read). The code would need
to be updated. Also, six member rings tend to adopt chair/boat/twist...
See for example Boeyens J. Cryst. Mol. Struct. 8, 317 (1978). Also Zotov
et al. JCICS 37, 766 (1997). There is a WWW pictorial description at:

  http://zefirov.ipac.ac.ru/eng/stereo_b.html

Google "pucker six-member ring" for more info, but note that ptraj cannot
at present calculate this (without code modification).

--tec3

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