Hello,
>
> I am analyzing number of solvent atoms within 3.5 Ang of residue No.
> 164. Following is the ptraj script which I tried to use, but it does not
> show any output. 451-585 are number of solvent molecules.
>
> trajin lyzargwat_MD2.crd
> distance a164 out a164.out [(:451-585.* <:3.5) & :164]
> go
This command will not do what you're looking to do. It will take the
center of mass of the first mask and find the distance between the
center of mass of the second mask, so you'll get only one distance
(though I'm not sure that the syntax for your distance command is
correct, you can check the manual for use of it).
The task you're attempting here sounds more like you need a radial
distribution function (see the radial keyword for ptraj in the
manual).
Good luck!
Jason
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Jan 14 2010 - 06:00:01 PST
