[AMBER] Vector command in cpptraj

From: Pietro Aronica <pietroa.bii.a-star.edu.sg>
Date: Mon, 16 Oct 2017 12:14:22 +0800


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


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Received on Sun Oct 15 2017 - 21:30:03 PDT
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