AMBER Archive (2007)

Subject: Re: SV: AMBER: Atoms in contact to a specific atoms during MD

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Rafi Ahmad wrote:
> Thanks for the reply.
>
> This is just for one trajectory and can be easily done with many other tools.
>
> But what I would like is to get it for all snapshots (i have 10000 of them). Meaning during all those snapshots what atoms are close to say atom "X".

This may not be totally correct, but you could also try ptraj's closest
command. There is a nice example of this command in action on p 250 of
the AMBER-9 Manual ( http://amber.scripps.edu/doc9/amber9.pdf )

regards,

Mark
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