Hi,
From the Amber 17 manual, cpptraj 'vector' command section 28.9.79 (pg 644):
"[out <filename>] Write vector data to <filename> with format ’Vx Vy
Vz Ox Oy Oz’ where V denotes vector coordinates and ’O’ denotes origin
coordinates."
Hope this helps. Let me know if you have more questions.
-Dan
On Mon, Oct 16, 2017 at 12:14 AM, Pietro Aronica
<pietroa.bii.a-star.edu.sg> wrote:
> Hello,
>
> I am working with a lipid bilayer, and I am trying to look at analysis
> commands in cpptraj to quantitatively examine my system. One of the
> things I am trying to do is monitor the position of a guanidine group on
> an arginine on an embedded peptide with respect to the hydrophilic heads
> of the lipids. My first instinct was to simply calculate distances
> between centres of mass but this method will show that distance is
> increasing if the guaninide is still near the heads but off-centre,
> which obviously not ideal.
>
> It was pointed out to me to use a vector command instead and use the
> z-component to determine the position of the guanidine group, but I need
> help interpreting the output. I used this command:
>
> vector mask out vector.dat @%N2 :49-192&:PC
>
> where .%N2 is to identify the guanidine group and :49-192&:PC the top
> leaflet's hydrophilic heads.
>
> The output is six numbers (technically 7, the first being the frame),
> and I am unsure what these represent. I think three are the vector
> origin and three are the x, y and z components of the vector, but which
> one is which? Is there something I am overlooking?
>
> I'm sorry if this sounds like a silly question but the manual does not
> specify and I couldn't find a clear, unambiguous explanation.
>
> Also, if I am going about this lipid analysis wrong, do tell me.
>
> Kind regards
>
> Pietro
>
>
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Mon Oct 16 2017 - 06:30:02 PDT
