AMBER Archive (2009)

Subject: Re: [AMBER] hbond analysis by ptraj- segmentation fault

From: Jayalakshmi Sridhar (
Date: Mon Nov 23 2009 - 12:36:25 CST

   <div style="font-family: 'Times New Roman'; font-size: 1 6px;"><br />Thank you Dan. I will get a new toppology file w ithout water and ions. I will try your suggestion of dividing the call into subsets. <br _moz_dirty="" />Jaya.<br _moz_ dirty="" /><br /><span>On 11/23/09, <b class="na me">Daniel Roe </b> &lt;; wrote:< /span><blockquotecite="" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite "><div class="mimepart text plain">Also, I just noticed this in your output:<br />&quot;Estimated memory usage for thi= s
   hbond call:  53.41 GB&quot;<br />Unless you have that mu= ch
   memory available ptraj will choke. Try dividing this call into subs= ets
   if possible.<br /><br />-Dan<br /><br />Jayalakshm= i
   Sridhar wrote:<br />&gt;   Dear Amber Users,<br /> &gt;   I am trying to do Hbond analysis using ptraj on the md tr ajectory file. I<br />&gt;   have stripped the trajectory = of
   water and ions. I have tried running the<br />&gt;   sc= ript
   on the .mdcrd file, but everytime I get the error- Segmentation fault<br />&gt;   (core dumped). I am attaching the outpu= t
   file and also the input file. Thank<br />&gt;   you for = the
   help in sorting out this problem.<br />&gt;   Jaya.<= br
   />&gt;  <br /><br />-- <br />Daniel R. Roe, P h.D.<br />Research Chemist<br />National Institute of Standa rds and Technology<br />100 Bureau Drive, Stop 8443<br />Gaith ersburg, MD 20899-8443<br />(301) 975-8741<br /><br /><b= r
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