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57151 Views 4 Replies Latest reply: Apr 3, 2013 12:28 PM by Jingjing Bu RSS
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Jun 4, 2010 7:48 AM

Hydrogen bond analysis

This is an enhanced version of the hydrogen bond script available in the scripting examples folder. It reads in structures in a study table and adds new columns to hold the following:

  • Number of hydrogen bonds
  • Average length of hydrogen bonds
  • Min length of hydrogen bonds
  • Max length of hydrogen bonds


It has been developed as an aid to analysis of Polymorph results but can, with a little modification, be used on any trajectory once inserted into a study table.

 

This only uses functionality available in the Materials Visualizer.

 

Best regards,

 

Stephen

Attachments:
  • javiersabe Master 77 posts since
    Jan 16, 2007
    Currently Being Moderated
    Jun 2, 2007 10:53 AM (in response to stodd)
    Re: Hydrogen bond analysis
    As usual thanks Stephen. It is great and vry useful.

    c heers

    Javier
  • mquak Novice 1 posts since
    Jan 17, 2012
    Currently Being Moderated
    Jan 17, 2012 3:37 PM (in response to stodd)
    Hydrogen bond analysis

    Hi Stephen,

     

    Could you guide me as to how to use this script for H-bond analysis? I have no experience with scripting so it is a little hard to start off with this file.

     

    I have a 400ps trajectory file (generated using Discovery) and would like to do an analysis using this script. No hydrogen bond calculation has been done so far. In order to use this script, is there any other calculations (pre-requisites) that need to be done in terms of the hydrogen bonds? "It reads in structures in a study table and adds new columns" - am not sure what a study table is and which file these columns are added into.

     

     

    Also what are the parts of the script I should modify? I've changed line 21 to my .xtd file name but that's it. Thanks!

     

    Michelle

  • Jingjing Bu Grand Master 116 posts since
    Oct 28, 2011
    Currently Being Moderated
    Apr 3, 2013 12:28 PM (in response to stodd)
    Re: Hydrogen bond analysis

    Hi Stephen

    What should I do if I want to modify your script to analyze H-bond between two sets of atoms? I tried to modify the setting to

     

    my $studyTable = $Documents{"$studyTableName.std"}->ActiveSheet;

    my $setA = $studyTable->Sets("H");

    my $setB = $studyTable->Sets("O");

     

    Then I got the following error when I debug:

     

    There is no function or property named "Sets" on type "Sheet" at -e line 28.

     

    on line:

     

    my $setA = $studyTable->Sets("H");

     

    Could you please help me out here? If my structure is periodic, should I add "UnitCell"?

     

    Thank you.

     

    Regards,

    Jingjing Bu

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