Date: Mon, 9 Jul 2018 16:17:43 +0530
Thank you for a prompt reply to my inquiry. I have a query. Is this second
column of my data is phi? When I am plotting this data, I did not get any
meaningful explanation. I attached the output file and the plot. Can anyone
please explain how to interpret the data?
thank you in advance
On Mon, Jul 9, 2018 at 3:08 PM, Rajarshi Roy <phd1701171011.iiti.ac.in>
wrote:
> Thank you for a prompt reply to my inquiry. I have a query. Is this second
> column of my data is phi? When I am plotting this data, I did not get any
> meaningful explanation. I attached the output file and the plot. Can anyone
> please explain how to interpret the data?
>
> thank you in advance
>
> On Mon, Jul 9, 2018 at 11:22 AM, Charles-Alexandre Mattelaer <
> camattelaer01.gmail.com> wrote:
>
>> Hi Rajarshi
>>
>> I use the pucker command from cpptraj. You can specify the atommask of the
>> six (or five) membered ring and it will calculate Cremer-Pople or Altona
>> puckering (in function of what you specified). Have a look at the correct
>> syntax in the manual!
>>
>> Kind regards
>>
>> Charles-Alexandre Mattelaer
>>
>> Op ma 9 jul. 2018 07:40 schreef Rajarshi Roy <phd1701171011.iiti.ac.in>:
>>
>> > Dear AMBER users and developers
>> >
>> > I want to estimate the different puckering states of carbohydrates in my
>> > simulation. Is there any tool for calculating Cremer-Pople parameters
>> > (theta, phi and Q) for pyranose ring like g_puckering tool in GROMACS?
>> >
>> > Thank you in advance
>> >
>> >
>> > --
>> >
>> > with regards
>> > Rajarshi Roy
>> >
>> > PhD Research Scholar
>> > Biosciences and Biomedical Engineering
>> > Indian Institute of Technology, Indore
>> > India
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
>
> with regards
> Rajarshi Roy
>
> PhD Research Scholar
> Biosciences and Biomedical Engineering
> Indian Institute of Technology, Indore
> India
>
-- with regards Rajarshi Roy PhD Research Scholar Biosciences and Biomedical Engineering Indian Institute of Technology, Indore India
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