AMBER Archive (2009)

Subject: RE: [AMBER] Hbond analysis output giving no hbonds

From: Jayalakshmi Sridhar (
Date: Tue Nov 24 2009 - 11:52:47 CST

   <div style="font-family: 'Times New Roman'; font-size: 1 6px;"><br />Thank you Mr. Thomas. Now I am getting the dat a.<br _moz_dirty="" />Jaya.<br _moz_dirty="" /><br /><span>On 11/24/09, <b class="name">Thomas Cheatham </b> &lt;; wrote:</span> <blockquotecite="mid:D1037AC94CF2B94DAF5B4EA5426C53F65511014322" class="iwcQuote" style=" border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; m argin-left: 0pt;" type="cite"><div class="mimepart t ext plain">Try adding the &quot;out&quot; keyword...< br /><br />hbond series hbt out hbond.dat \<br />   ti= me
   1.0 angle -1.0 distance 3.1<br /><br />&gt;   I=  
   am trying to get Hbond analysis using ptraj of an MD run. Since th= e<br
   />&gt;   protein  is large, the memory needed was h= uge.
   So, I am trying to call<br />&gt;   subsets of atom= s to
   reduce memory requirement. It looks like the run is<br />&g t;   going to completion successfully, but the output does not s how any Hbonds. I<br />&gt;   am attaching the input and o utput files. Help is greatly appreciated. Thank<br />____ ________________________ ___________________<br/>AMBER mailing list<br /><br /><

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