AMBER Archive (2004)

Subject: AMBER: H-bonded waters selection

From: pl (ladam_at_smbh.univ-paris13.fr)
Date: Thu Nov 04 2004 - 06:41:32 CST

Hi all,

Here is a beginner question I guess...
I have a trajectory of solvated DNA and I want to analyse the hydration
of my DNA. For this I'd like to re-save this trajectory with the DNA
plus the water molecules that are H-bonded to it (that is get rid of
waters not H-bonded to DNA and visualize with VMD). I tried to play
around with ptraj and the trajout command but could not acheive that.
If someone has an answer...
Thank you very much
Bye all

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| Patrick LADAM | |
| Laboratoire CSSB | THE BIG BANG THEORY: |
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