[AMBER] Lipid NMR order parameters

From: Christopher Faulkner <FaulknerC3.cardiff.ac.uk>
Date: Tue, 10 Jul 2018 12:53:30 +0000

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 Tue Jul 10 2018 - 06:00:02 PDT
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