Hi,
That does seem strange, but I suppose it could be possible. What
version of cpptraj does this happen with?
-Dan
On Sun, Dec 16, 2018 at 8:00 PM Baker, Joseph <bakerj.tcnj.edu> wrote:
>
> Hi Dan and Christopher,
>
> A quick follow up to this question. When using lipidscd to perform a
> calculation of the order parameters for a POPE lipid system, the standard
> deviation columns report values ~ equal to the reported order parameters
> themselves. Is this expected?
>
> Thanks for your input.
>
> Kind regards,
> Joe
>
> ------
> Joseph Baker, PhD
> Assistant Professor
> Department of Chemistry
> C101 Science Complex
> The College of New Jersey
> Ewing, NJ 08628
> Phone: (609) 771-3173
> Web: http://bakerj.pages.tcnj.edu/
>
> Chair-elect (2018), Trenton Local Section of the ACS
> Chemistry Division Councilor (2018-2021), The Council on Undergraduate
> Research
>
>
>
> On Thu, Jul 12, 2018 at 3:16 AM Christopher Faulkner <
> FaulknerC3.cardiff.ac.uk> wrote:
>
> > Hi Daniel,
> >
> >
> > Thanks for your helpful suggestion, this works very well.
> >
> >
> > Cheers,
> >
> > Christopher
> >
> > ________________________________
> > From: Daniel Roe <daniel.r.roe.gmail.com>
> > Sent: 10 July 2018 17:12:38
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] Lipid NMR order parameters
> >
> > Hi,
> >
> > Try the 'lipidscd' command, which performs the same calculation but
> > has a slightly easier-to-use syntax. This command will automatically
> > identify unique chains for you.
> >
> > lipidscd out ordertest2.dat
> >
> > Hope this helps,
> >
> > -Dan
> >
> > On Tue, Jul 10, 2018 at 8:53 AM, Christopher Faulkner
> > <FaulknerC3.cardiff.ac.uk> wrote:
> > > Dear all,
> > >
> > >
> > > I am trying to calculate the NMR parameters for the sn1 and sn2 chains
> > in my DOPC lipid bilayer. I notice that the sn1 and sn2 chains have the
> > same residue name ":OL". So when I use the lipidorder command in cpptraj:
> > >
> > >
> > > trajin 125DOPC.crd
> > > lipidorder out ordertest2.dat z \
> > > ":OL.C12" ":OL.C13" ":OL.C14" ":OL.C15" ":OL.C16" ":OL.C17" ":OL.C18"
> > ":OL.C19" ":OL.C110" ":OL.C111" ":OL.C112" ":OL.C113" ":OL.C114"
> > ":OL.C115" ":OL.C116" ":OL.C117" ":OL.C118"
> > >
> > > I get values which I presume are for all of the chains, not just the
> > sn1. Is there a way I can differentiate between the chains?
> > >
> > > Any help is much appreciated,
> > >
> > > Christopher Faulkner
> > >
> > > PhD student
> > >
> > > Cardiff University
> > >
> > >
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Received on Fri Dec 21 2018 - 12:00:03 PST
