Previously , you mentioned as the following : If you are using cpptraj you
can add the'center1' keyword to calculate the RDF from the center of mass
ofresidues 1 to 229 to all atoms in residues named WAT, e.g.
radial 0.05 12 :1-229 :WAT center1
According to this, my input file was rewritten as:
trajin ***.mdcrd
center origin :1-229
image origin center
radial 0.05 12 :1-229 :WAT center1
the command during the calculation is£ºAMBERHOME/exe/cpptraj ***.prmtop
rdf.in
attention BEGIN TRAJECTORY PROCESSING:
----- [last20ns.mdcrd] (1-9901, 100) -----
.... Setting up 2 actions for wat-wat.prmtop ....
...................................................
[||||||||||||||||||||||||||||||||||||||||||||||||||] Complete.
Read 100 frames and processed 100 frames.
OUTPUT:
DATASETS:
There are no data sets.
NO DATASETS WILL BE OUTPUT
I would like to know whether my input file was wrong or the command was
used in an unreasonable way. I haven¡¯t found the tools which could
calculate RDF in the test of cpptraj .I want to know whether cpptraj
support RDF ? I am looking for your replay.
Thank you for you help again .
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Received on Tue Sep 11 2012 - 19:00:05 PDT
