Hi,
On Mon, Aug 26, 2013 at 2:14 PM, mish <smncbr.gmail.com> wrote:
> 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) ?
Unfortunately, you can't right now. This is an item on my to-do list
that I hope to have accomplished by the next release.
-Dan
>
> 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
>> > (801) 585-9119 (Fax)
>> >
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>>
>>
>>
>> --
>> *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
(801) 585-9119 (Fax)
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Received on Mon Aug 26 2013 - 14:30:02 PDT
