AMBER Archive (2006)

Subject: Re: AMBER: Closest(closest water)

From: Adrian Roitberg (
Date: Mon Oct 30 2006 - 07:12:13 CST

Sergey Samsonov wrote:
> 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,
> Sergey

First, I expect that the output traj will have box info, unless you
explicitely write nobox there.

More importantly, what top file are you using to visualize ?
You should not be using the original one with all the waters, since your
new trajectory only has ten of them.

So, create a new top file with just ten waters, out of a pdb file, and
look again.

When things like this happen, it is always useful to LOOK into the mdcrd
file to see what numbers are in there.


                            Dr. Adrian E. Roitberg
                              Associate Professor
               Quantum Theory Project and Department of Chemistry

University of Florida PHONE 352 392-6972 P.O. Box 118435 FAX 352 392-8722 Gainesville, FL 32611-8435 Email ============================================================================

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