On Mon, Jun 17, 2019 at 3:48 PM Steven M. Graham <grahams.stjohns.edu> wrote:
>
> Hi all:
> There is a slight difference in the AS and CP values of puckering. There is a reasonable description is the PSEUROT 6.3 manual, which I have if anyone wants a copy.
See also the following paper from Rao et al.:
http://scripts.iucr.org/cgi-bin/paper?S0567739481000892
-Dan
> Steve
>
> -----Original Message-----
> From: Charles-Alexandre Mattelaer [mailto:camattelaer01.gmail.com]
> Sent: Monday, June 17, 2019 9:44 PM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Amplitude of ring puckering
>
> * External Email *
>
> Hi
>
> Thank you for the clarification!
>
> Kind regards
>
> Charles-Alexandre Mattelaer
>
> Op ma 17 jun. 2019 21:41 schreef Daniel Roe <daniel.r.roe.gmail.com>:
>
> > Hi,
> >
> > On Sat, Jun 15, 2019 at 9:00 AM Charles-Alexandre Mattelaer
> > <camattelaer01.gmail.com> wrote:
> > > expect this to be an angle but since the reported values in cpptraj
> > > are only small I suspect this to be in radians. Would someone be so
> > > kind to
> >
> > Yeah, the amplitude values are not converted to degrees - I think that
> > was an oversight on my part. According to the equations for A-S
> > (assuming I'm reading them right) the amplitude amp (where amp =
> > sqrt(A^2+B^2) should be in radians since A and B are in radians. I
> > think same thing for C-P as well, although I'm going to double check
> > that. Note that theta for C-P is actually converted to degrees, so its
> > only the amplitude values that have this issue.
> >
> > -Dan
> >
> > > comment on my suspicion? I checked the manual but it isn't mentioned
> > > in what unit the amplitude is reported.
> > >
> > > Is it also the case for the Cremer nomenclature that the amplitude
> > > in
> > this
> > > definition is the 'out-of-plane displacement'?
> > >
> > > Thanks in advance!
> > >
> > > Charles-Alexandre Mattelaer
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Received on Tue Jun 18 2019 - 09:30:04 PDT
