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From: Hurt, Darrell (NIH/NIAID) [E] (darrellh_at_niaid.nih.gov)
Date: Thu Apr 08 2010 - 15:32:18 CDT

I tweaked the code by commenting out the loop:

# if { [lsearch { "OD1" "OD2" "OE1" "OE2" "OT1" "OT2" "NH1"
"NH2" } $atomname] != -1 } {
# lappend newhbond_donor "-[string range $atomname 0 1]"
# } else { lappend newhbond_donor "-$atomname" }

and replacing it by simply:

            lappend newhbond_donor "-$atomname"

This gives me the results I want. Does anyone want to comment on whether
there is some theoretical or logical argument against doing it this way?

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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> From: "Hurt, Darrell (NIH/NIAID) [E]" <darrellh_at_niaid.nih.gov>
> Date: Thu, 8 Apr 2010 12:48:39 -0400
> To: "vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>
> Subject: vmd-l: Hydrogen bonds plugin obscures charged atoms -- help!
>
> Hi there,
>
> This may be a question for James Gumbart or Dong Luo, who together wrote the
> plugin.
>
> I¹m 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. I¹m not sure why ‹ perhaps because they are
> chemically equivalent. Maybe I¹m not getting something. Anyway, here¹s an
> example of what I think may be the offending line:
>
> if { [lsearch { "OD1" "OD2" "OE1" "OE2" "OT1" "OT2" "NH1" "NH2" } $atomname]
> != -1 } {
>
> Unfortunately, I¹m 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)
>
> Disclaimer: The information in this e-mail and any of its attachments is
> confidential and may contain sensitive information. It should not be used by
> anyone who is not the original intended recipient. If you have received this
> e-mail in error please inform the sender and delete it from your mailbox or
> any other storage devices. National Institute of Allergy and Infectious
> Diseases shall not accept liability for any statements made that are
> sender's own and not expressly made on behalf of the NIAID by one of its
> representatives.
>
>
>