Parviz,
see my answer for your 2nd question.
On Thu, Jun 30, 2016 at 12:20 PM, Parviz Seifpanahi Shabane <sparviz.vt.edu>
wrote:
> 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?
>
You can write to new stripped trajectory and topology
parm tz2.ortho.parm7
trajin tz2.ortho.nc
closest 10 :1-12 parmout *my.parm7*
trajout* my.nc <
http://my.nc>*
Then use *my.nc <
http://my.nc>, my.parm7* for further analysis:
https://github.com/hainm/amber_things/issues/19
(shameless advertising for our visualization program)
Hai
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Received on Thu Jun 30 2016 - 19:30:03 PDT
