Thanks for the conformation. I looked through the amber archives and
people had done something or asked about
pyranose rings
AMBER Archive (2005) - Re: AMBER: Pyranose pucker parameters
I am trying to determine the pucker parameters of neuraminic acid from
an ... pucker parameters. Here are the first 8 lines of my output: ...
structbio.vanderbilt.edu/archives/amber-archive/.../1564.php -
and was confused as the torsion.c in ptraj were asking for 5 sets of
xyz coordinates.
Could it still be changedby making the code read 6 sets of xyz
coordinates and then
using
a = (v1*cos(0.0) +
v2*cos( 4.0*PI/5.0) +
v3*cos( 8.0*PI/5.0) +
v4*cos(12.0*PI/5.0) +
v5*cos(16.0*PI/5.0)
v6*cos(20.0*PI/5.0))*0.4; and so on
thanks for the help.
regards,
ganesh
On Fri, Oct 16, 2009 at 2:23 PM, Thomas Cheatham III <tec3.utah.edu> wrote:
>
> > 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.C6 :233.C7 :233.N8 :233.C8A :233.C4A :233.N5 out
> > puckerDHPpseudo.dat cremer offset -90.0
> > pucker name2 :233.C6 :233.C7 :233.N8 :233.C8A :233.C4A :233.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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Received on Fri Oct 16 2009 - 12:00:03 PDT
