Re: [AMBER] lipid order per leaflet

From: Daniel Roe <>
Date: Fri, 13 Sep 2019 12:22:40 -0400


Sorry for the late reply on this.

You may want to try the 'lipidscd' command, which also calculates
lipid order parameters but supports mask selection. So e.g.

lipidscd L1OL :1-40&:OL out L1OL.dat
lipidscd L1PA :1-40&:PA out L1PA.dat

(Assuming your first leaflet is residues 1 - 40; adjust as necessary).

Hope this helps,


On Tue, Sep 3, 2019 at 1:49 PM Violeta Burns Casamayor
<> wrote:
> Hi,
> I'm trying to calculate the lipid order parameters of OL and of PA
> separately and I wanted to split that calculation per leaflet (z>0 or z<0).
> however, I can't seem to find the right mask to make it work.
> This is what I have so far:
> lipidorder out output-OL.dat scd ":OL.C12" ":OL.H2R" ":OL.H2S" ":OL.C13"
> ":OL.H3R" ":OL.H3S" ":OL.C14" ":OL.H4R" ":OL.H4S" ":OL.C15" ":OL.H5R"
> ":OL.H5S" ":OL.C16" ":OL.H6R" ":OL.H6S" ":OL.C17" ":OL.H7R" ":OL.H7S"
> ":OL.C18" ":OL.H8R" ":OL.H8S" ":OL.C19" ":OL.H9R" ":OL.H9R" ":OL.C110"
> ":OL.H10R" ":OL.H10R" ":OL.C111" ":OL.H11R" ":OL.H11S" ":OL.C112" ":OL.H12R"
> ":OL.H12S" ":OL.C113" ":OL.H13R" ":OL.H13S" ":OL.C114" ":OL.H14R" ":OL.H14S"
> ":OL.C115" ":OL.H15R" ":OL.H15S" ":OL.C116" ":OL.H16R" ":OL.H16S" ":OL.C117"
> ":OL.H17R" ":OL.H17S" ":OL.C118" ":OL.H18R" ":OL.H18S"
> run
> Any suggestions?
> thanks.
> Violetta Burns
> PhD student
> Mertz Group
> WVU Department of chemistry
> "*Every great and deep difficulty bears in itself its own solution. It
> forces us to change our thinking in order to find it." - Niels Bohr*
> *“You do not really understand something unless you can explain it to your
> grandmother.” - Albert Einstein*
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Received on Fri Sep 13 2019 - 09:30:02 PDT
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