Dear Amber User, I want to calculate the correlation function for first
water shell (water molecules which have H-bonds with protein) around
protein, at first, I used the closest command with mask of Oxygen (.O) for
finding the nearest water molecules to oxygen atoms in protein ( assuming
those water molecules have H-bonds with protein) in next step I want to use
the vector command for calculating the dipole moment of this water
molecules, but problems is I do not know how to use the output of the
closest command as input for vector command ( I used the read data but it
was not given anythings)
first of all, I want to know that my method is correct or not?
second how to use the output of closest as input for vector command?
Best
Parviz
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Received on Thu Jun 30 2016 - 09:30:02 PDT
