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 - 10:00:03 PDT
