Any chance you could send me off-list a topology and 1 or 2 frames so
I can try to figure out whats going on? May be there's a bug, or
there's some other reason the code isn't working as expected.
Thanks!
-Dan
On Mon, Sep 16, 2019 at 12:37 PM Violeta Burns Casamayor
<vb0009.mix.wvu.edu> wrote:
>
> Hi Dan,
>
> It seems that it doesn't work if i put the selection in the way you
> mentioned:
>
> lipidscd L1OL :1-40&:OL out L1OL.dat
> lipidscd L1PA :1-40&:PA out L1PA.dat
>
> but it gives me the following output:
> 0 chains
> 0 chains type:
>
> however, if i only use the residue numbers per leaflet, it slips it between
> PA and OL chains:
>
> Mask [:261-485] corresponds to 10050 atoms.
> 149 chains.
> 2 chain types:
> [0] 75 chains, Residue PA, carboxyl atom C11 (15 carbons)
> [0] 75 chains, Residue PA, carboxyl atom C11 (15 carbons)
> Pos. Name #H
> 2 C12 2
> 3 C13 2
> 4 C14 2
> 5 C15 2
> 6 C16 2
> 7 C17 2
> 8 C18 2
> 9 C19 2
> 10 C110 2
> 11 C111 2
> 12 C112 2
> 13 C113 2
> 14 C114 2
> 15 C115 2
> 16 C116 3
> [1] 74 chains, Residue OL, carboxyl atom C21 (17 carbons)
> Pos. Name #H
> 2 C12 2
> 3 C13 2
> 4 C14 2
> 5 C15 2
> 6 C16 2
> 7 C17 2
> 8 C18 2
> 9 C19 1
> 10 C110 1
> 11 C111 2
> 12 C112 2
> 13 C113 2
> 14 C114 2
> 15 C115 2
> 16 C116 2
> 17 C117 2
> 18 C118 3
>
>
> 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*
>
>
>
> On Fri, Sep 13, 2019 at 12:23 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> > Hi,
> >
> > 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,
> >
> > -Dan
> >
> > On Tue, Sep 3, 2019 at 1:49 PM Violeta Burns Casamayor
> > <vb0009.mix.wvu.edu> 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 Mon Sep 16 2019 - 10:30:02 PDT
