RE: [AMBER] Hbond analysis output giving no hbonds from Jayalakshmi Sridhar on 2009-11-24 (Amber Archive Nov 2009)

From: Jayalakshmi Sridhar <jsridhar.xula.edu>
Date: Tue, 24 Nov 2009 11:52:47 -0600

<div style="font-family: 'Times New Roman'; font-size: 1 6px;"> Thank you Mr. Thomas. Now I am getting the dat a. Jaya. On 11/24/09, Thomas Cheatham <tec3.utah.edu> wrote: <blockquotecite="mid:D1037AC94CF2B94DAF5B4EA5426C53F65511014322 .C5V1.xds.umail.utah.edu" 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 "out" keyword... hbond series hbt out hbond.dat \ ti= me
 1.0 angle -1.0 distance 3.1 > I=
 am trying to get Hbond analysis using ptraj of an MD run. Since th= e > protein is large, the memory needed was h= uge.
 So, I am trying to call > subsets of atom= s to
 reduce memory requirement. It looks like the run is &g t; going to completion successfully, but the output does not s how any Hbonds. I > am attaching the input and o utput files. Help is greatly appreciated. Thank ____ ________________________ ___________________ AMBER mailing list AMBER.ambermd.org <a href="htt p://lists.ambermd.org/mailman/listinfo/amber"target="_bla nk">http://lists.ambermd.org/mailman/listinfo/amber</a><
 /></div></blockquote></div>

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Received on Tue Nov 24 2009 - 10:00:03 PST