AMBER Archive (2009)

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

From: Ganesh Kamath (gkamath9173_at_gmail.com)
Date: Fri Oct 16 2009 - 13:36:41 CDT

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

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