<div>Hi</div>
<div>When I run dssp alone with a .pdb file it works well. But when I run with Gromacs as do_dssp it gives segmentation fault and does not do any calculation except giving some intermediate files as follows.</div>
<div><br>
<p>Opening library file /usr/local/gromacs/share/gromacs/top/ss.map<br>Reading frame 0 time 0.000<br>Warning: if there are broken molecules in the trajectory file,<br> they can not be made whole without a run input file<br>
<br> <br>Back Off! I just backed up dd8G1JXX to ./#dd8G1JXX.1#<br>Segmentation fault</p>
<p>shahid </p><br> </div>
<div><span class="gmail_quote">On 5/18/10, <b class="gmail_sendername">Justin A. Lemkul</b> <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>> wrote:</span>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><span class="q"><br><br>shahid nayeem wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Hi<br>After posting this mail I did some google search and after changing the executible name to dssp I moved it in /usr/local/bin/ After this when I did do_dssp it starts running asks to select a group I choose main chain 5, then it generates some intermediate file and gives error as segmentation fault. I though this problem was because of the executible in /usr/local/bin/ and rest of file in another directory say /home/shahid/software/dssp/. For this first I set the path in ~/.bascrc <br>
</blockquote><br></span>Other files should be irrelevant. The only file you need is the dssp binary.<span class="q"><br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">as DSSP=/home/shahid/software/dssp/DsspCmbi. I tried to run do_dssp I got the same intermediate file generated backing up the previous one. <br>
</blockquote><br></span>Intermediate files are not an issue. When the executable is in this directory, does the calculation otherwise work?<span class="q"><br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Then I moved all the files of dssp directory to /usr/local/bin/ and then tried to run do_dssp I am in the same situation.<br>
</blockquote><br></span>If the executable in your home directory structure works, but in /usr/local/bin it fails, then it could be some sort of permission error. It ultimately doesn't matter where your executable is, /usr/local/bin is default, but you can set any other location you like with the DSSP environment variable.<br>
<br>-Justin<br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid"><span class="q">waiting for your help<br>shahid nayeem<br><br></span>
<div><span class="e" id="q_128ab4f8bcffa3d3_7"> On 5/18/10, *Justin A. Lemkul* <<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br><br><br> shahid nayeem wrote:<br><br> Dear All<br> I downloaded dsspcmbi.tar.gz, and compiled using command<br> ./DsspCompileGCC as given in Readme.txt file. when I try to run<br> do_dssp command in gromacs I get error<br>
<br><br> Well, what happened?<br><br><br> Fatal error:<br> DSSP executable (/usr/local/bin/dssp) does not exist (use setenv<br> DSSP)<br><br> I checked for DSSP executible in /usr/local/bin/ and I couldnt<br>
find. I<br><br><br> It won't be there unless you put it there and you have re-named it.<br> I believe the default name of the dssp program is "dsspcmbi," which<br> you need to change when you move the executable.<br>
<br> <a onclick="return top.js.OpenExtLink(window,event,this)" href="http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp" target="_blank">http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp</a><br>
<br> -Justin<br><br> even tried dsspcmbi.zip file but again I got the same error. I<br> compiled dssp as root. Now what shoul I do in order to run do_dssp<br> comand of gromacs.<br> Shahid nayeem<br>
<br><br> -- ========================================<br><br> Justin A. Lemkul<br> Ph.D. Candidate<br> ICTAS Doctoral Scholar<br> MILES-IGERT Trainee<br> Department of Biochemistry<br> Virginia Tech<br> Blacksburg, VA<br>
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<div><span class="e" id="q_128ab4f8bcffa3d3_15"><br>-- <br>========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>
Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]<a onclick="return top.js.OpenExtLink(window,event,this)" href="http://vt.edu/" target="_blank">vt.edu</a> | (540) 231-9080<br><a onclick="return top.js.OpenExtLink(window,event,this)" href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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