AMBER Archive (2006)

Subject: AMBER: Closest(closest water)

From: Sergey Samsonov (
Date: Mon Oct 30 2006 - 06:58:11 CST

Dear Amber users,

maybe someone of you had already faced this kind of problem. I've been
trying to use "closest" command to see the behavior of the closest water
molecules near the residues of interest. I used ptraj input file like this:

trajin ../mdcrd/imaged_trajectory.mdcrd 1 1000 1
trajout closest10.mdcrd trajectory
solvent byres :WAT
closestwater 10 :12 first

The trajectory is written in to the outfile but it looks like the one as
when you download AMBER Coordinate instead of AMBER Coordinates with
Periodic Box. Really long and incorrect bonds are appearing. I also
tried some different combinations of the input, applied them to both
imaged and not imaged trajectories but still the result is the same. My
system is under periodic boundary conditions.

Thank you very much for the answer in advance!

Best regards,


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