I want to add a question here, how can we use this "pucker" command in
ptraj/cpptraj for pyranoses ( 6 six-membered ring consisting of five carbon
atoms and one oxygen) ?
Thanks
Mish
On Mon, Aug 26, 2013 at 9:46 PM, arundhati dutta <arundhatidut.gmail.com>wrote:
> Hello,
>
> Thanks for the help.
>
> Arundhati
>
>
> On Mon, Aug 26, 2013 at 2:42 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
>
> > Hi,
> >
> > You can get a slightly more detailed analysis of pucker values in
> > cpptraj by using the 'statistics' analysis. For example:
> >
> > pucker p1-as :274.C1' :274.C2' :274.C3' :274.C4' :274.O4'
> > statistics p1-as out p1-as.stat.dat
> >
> > In 'p1-as.stat.dat' you will get the % occupied for various pucker
> > types, as well as torsion average and std. deviation. See the manual
> > for some more details.
> >
> > Hope this helps,
> >
> > -Dan
> >
> > On Mon, Aug 26, 2013 at 10:31 AM, arundhati dutta
> > <arundhatidut.gmail.com> wrote:
> > > Hello,
> > >
> > > Is there any way to know the type of sugar puckering. I have used the
> > > pucker command but it gave me some bunch of numerical data.
> > >
> > > Thank You
> > > Arundhati
> > >
> > > --
> > > *A.Dutta (PPG INSTITUTE OF TECH ,MCA)
> > > *
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> >
> >
> > --
> > -------------------------
> > Daniel R. Roe, PhD
> > Department of Medicinal Chemistry
> > University of Utah
> > 30 South 2000 East, Room 201
> > Salt Lake City, UT 84112-5820
> > http://home.chpc.utah.edu/~cheatham/
> > (801) 587-9652
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> >
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>
>
>
> --
> *A.Dutta (PPG INSTITUTE OF TECH ,MCA)
> *
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Received on Mon Aug 26 2013 - 13:30:03 PDT
