Dear sir,
I use maltoside as a building block of my bilayer system.
This molecule has two sugar rings (ring1 and rng2) attached via a
glycosidic oxygen.
Now I wish to calculate how closely the sugars are arranged at the
headgroup region.
For that I would like to calculate the RDF for the reducing and non
reducing sugar rings separately.
Normally we define an atom mask at one particular residue site and may be
choose a solvent to calculate the RDF.
But here I am thinking of getting a center of mass for each sugar ring unit
and calculate the RDF of them.
Is this possible to acheive via cpptraj command?
I am thinking of command such as
radial ring1_Out.rdf 0.05 15.0 :DDM.O11 O12 O13 O14 O15 O16 :DDM.O21 O22
O23 O24 O25 O26 noimage center1 center2 nointramol
Could the above command calculate what I want?
Many thanks in advance.
Vijay
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Received on Mon Apr 06 2015 - 20:00:02 PDT
