AMBER Archive (2006)

Subject: Re: AMBER: Closest(closest water)

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
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
>

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.

Cheers
a. 

-- 
                            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 adrian_at_qtp.ufl.edu
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