AMBER Archive (2009)

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

From: Ganesh Kamath (
Date: Mon Oct 19 2009 - 12:42:17 CDT

Thanks Bill. I ran the carnal with analin. A question comes as in the output is
L0 4.670143e-02 2.188132e+02 1.754455e-02
L0 3.509093e-02 2.200238e+02 3.836253e-02
L0 6.396239e-02 3.068664e+02 5.300770e-03
L0 1.539782e-01 2.853569e+02 3.012650e-03
L0 1.104845e-01 2.803663e+02 -3.327869e-03
L0 9.261769e-02 2.268125e+02 -8.909780e-02
L0 8.826193e-02 2.053027e+02 -8.114358e-02

Does this mean amplitude puckerangle and then what is the third column.
A second question is in the analin input file does it matter what
order I give to the atoms for whom the pucker needs to be



On Fri, Oct 16, 2009 at 3:48 PM, Bill Ross <> wrote:
>> I think i have a version of carnal from AMBER 8. How could I go about using
>> it for calculating the pucker for six member ring.
> You'd have to read the manual - there should be an example there.
> Bill
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