From: Hurt, Darrell (NIH/NIAID) [E] (darrellh_at_niaid.nih.gov)
Date: Thu Apr 08 2010 - 11:48:39 CDT

Hi there,

This may be a question for James Gumbart or Dong Luo, who together wrote the
plugin.

Iım trying to track hydrogen bonds for an aspartate that is hydrogen bonded
(or salt bridged) to up to three other arginines. The problem is that the
side chain of aspartate can hydrogen bond at two locations and the side
chain of arginine can hydrogen bond at three. Unfortunately, the ³Detailed
hbond data² file from the plugin truncates the atom names so that I cannot
tell precisely where the hydrogen bonds are. Here is my output file:

Found 5 hbonds.
donor acceptor occupancy
SegW-water-O SegP1-ASP142-Side-OD 62.87%
SegP1-ARG159-Side-NH SegP1-ASP142-Side-OD 59.90%
SegP1-ARG159-Side-NE SegP1-ASP142-Side-OD 75.25%
SegP1-ARG143-Side-NH SegP1-ASP142-Side-OD 0.99%
SegP1-ARG163-Side-NH SegP1-ASP142-Side-OD 77.72%

As you can see, the OD atoms of the ASP are engaged in hydrogen bonds more
than 100% of the time. That's OK, I guess, because hydrogen bond acceptors
can accept two bonds at a time. The problem is that I want to know exactly
which atoms are engaged in the bonding. I could resolve the ambiguity if the
atom was explicitly designated (e.g. OD1 or OD2).

I think the trouble goes back to the script which seems to toss out the
explicit designations. Iım not sure why ‹ perhaps because they are
chemically equivalent. Maybe Iım not getting something. Anyway, hereıs an
example of what I think may be the offending line:

if { [lsearch { "OD1" "OD2" "OE1" "OE2" "OT1" "OT2" "NH1" "NH2" } $atomname]
!= -1 } {

Unfortunately, Iım not sure how to alter the code. I would really appreciate
either an explanation of the thinking behind this line or some help on how
to explicitly list the atom-by-atom hydrogen bonds.

For completeness, here is the listing of my input parameters:

H-Bonds Plugin, Version 1.1
Thu Apr 08 11:35:36 EDT 2010

Parameters used in the calculation of hydrogen bonds:
- Atomselection 1: (sidechain and resid 142) and (name "N.*" "O.*" "S.*" FA
F1 F2 F3)
- Atomselection 2: (not (sidechain and resid 142)) and (name "N.*" "O.*"
"S.*" FA F1 F2 F3)
- Update selections every frame: yes
- Initial frame: 0
- Frame step: 1
- Final frame: 201
- Donor-Acceptor distance: 3.0
- Angle cutoff: 20
- Type: unique
- Write a file with H bond/frame data: yes
- Filename: hbonds.dat
- Details output file: C-YF_142.txt

Much thanks!

Darrell

Darrell Hurt, Ph.D.
Section Head, Computational Biology
Bioinformatics and Computational Biosciences Branch (BCBB)
OCICB/OSMO/OD/NIAID/NIH
 
31 Center Drive, Room 3B62
Bethesda, MD 20892
Office  301-402-0095
Mobile 301-758-3559
http://bioinformatics.niaid.nih.gov (Within NIH)
http://exon.niaid.nih.gov (Public)

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