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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> > AMBER.ambermd.org
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>
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Received on Sun Dec 16 2018 - 17:30:02 PST
