AMBER Archive (2009)

Subject: [AMBER] Amber: water-water hydrogen bonding analysis on a subset of waters in a trajectory

From: Jeff Schwinefus (
Date: Tue Mar 03 2009 - 16:18:25 CST


My current simulation contains a single mononucleotide, 5 Na+ and 5
Cl- ions, 20 urea molecules and 1093 TIP3P waters. My goal is to
perform a hydrogen bond analysis between water molecules within 6
angstroms of the mononucleotide AND beyond 6 angstroms of the
mononucleotide to characterize water-water hydrogen bonds in a "local"
domain and a "bulk" domain.

Can ptraj perform such an analysis? So far, I have thought of two
ways to attack this problem.

1) Using ptraj, I have tried hbond. The ptraj input script I have
used to analyze just donor water-water hydrogen bonds within 6
angstroms of my mononucleotide (residues :1-2; :1 represents the
phosphate, :2 the sugar and base) is:

trajin AMP2md.mdcrd.gz

center :1-2 mass origin
image origin center familiar
rms first mass :1-2

# water donor
donor mask "(:1-2 < @6) & :WAT_at_O"

hbond distance 3.5 angle 120 solvent nieghbor 6 solventacceptor WAT O
H1 solventacceptor WAT O H2 time 1.0 series hbww out

This script generates a segmentation fault. I have tried 3.5
angstroms as the distance from the mononucleotide to test with fewer
waters, but I still get the segmentation error. I suppose I could be
running out of memory even using 3.5 angstroms. My script might also
have an error. Regardless, I guess that the donor mask does not
reselect waters every frame. Is this correct? In that case, I
suppose I could write a script to determine the hydrogen bonds for
each frame.

2) I have thought about using "closest" command in ptraj to select the
N closest waters (based on a previous "watershell" test run), create a
pdb file after "closest", create a new prmtop file, then analyze the
hydrogen bonds between water. However, if I use this method, how do I
analyze hydrogen bonds for those waters that are 6 angstroms or
further from the mononucleotide?

Thanks for taking time to help.


Jeff Schwinefus
Associate Professor of Chemistry
St. Olaf College
Northfield, MN 55057
(507) 786-3105
FAX (507) 786-3968

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