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<p class=MsoNormal><span class=EmailStyle20><font size=2 color=navy face=Arial><span
style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Arial'><span
style="mso-spacerun:
yes">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
</span>Shahid,<o:p></o:p></span></font></span></p>

<p class=MsoNormal><span class=EmailStyle20><font size=2 color=navy face=Arial><span
style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></font></span></p>

<p class=MsoNormal style='margin-left:33.0pt'><span class=EmailStyle20><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;mso-bidi-font-size:
12.0pt;font-family:Arial'>Before trying for &#8220;do_dssp&#8221; a gromacs utility calling
dssp program , try first dssp program itself<span style="mso-spacerun:
yes">&nbsp; </span>by passing simple input like pdb and I hope by that way you
can resolve your problem<o:p></o:p></span></font></span></p>

<p class=MsoNormal style='margin-left:33.0pt'><span class=EmailStyle20><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;mso-bidi-font-size:
12.0pt;font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></font></span></p>

<p class=MsoNormal style='margin-left:33.0pt'><span class=EmailStyle20><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;mso-bidi-font-size:
12.0pt;font-family:Arial'>B.Nataraj<o:p></o:p></span></font></span></p>

<p class=MsoNormal><span class=EmailStyle20><font size=2 color=navy face=Arial><span
style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></font></span></p>

<p class=MsoNormal><span class=EmailStyle20><font size=2 color=navy face=Arial><span
style='font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Arial'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></font></span></p>

<p class=MsoNormal style='margin-left:.5in'><font size=2 color=black
face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma;color:black'>-----Original
Message-----<br>
<b><span style='font-weight:bold'>From:</span></b>
gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org]<b><span
style='font-weight:bold'>On Behalf Of </span></b>shahid nayeem<br>
<b><span style='font-weight:bold'>Sent:</span></b> Tuesday, May 18, 2010 5:17
PM<br>
<b><span style='font-weight:bold'>To:</span></b> jalemkul@vt.edu; Discussion
list for GROMACS users<br>
<b><span style='font-weight:bold'>Subject:</span></b> Re: [gmx-users] DSSP</span></font></p>

<p class=MsoNormal style='margin-left:.5in'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'><![if !supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></font></p>

<p class=MsoNormal style='margin-left:.5in'><font size=3 color=black
face="Times New Roman"><span style='font-size:12.0pt;color:black'>Hi</span></font><font
color=black><span style='color:black;mso-color-alt:windowtext'><o:p></o:p></span></font></p>

<p class=MsoNormal style='margin-left:.5in'><font size=3 color=black
face="Times New Roman"><span style='font-size:12.0pt;color:black'>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 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. 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. </span></font><font color=black><span
style='color:black;mso-color-alt:windowtext'><o:p></o:p></span></font></p>

<p class=MsoNormal style='margin-left:.5in'><font size=3 color=black
face="Times New Roman"><span style='font-size:12.0pt;color:black'>waiting for
your help</span></font><font color=black><span style='color:black;mso-color-alt:
windowtext'><o:p></o:p></span></font></p>

<p class=MsoNormal style='margin-left:.5in'><font size=3 color=black
face="Times New Roman"><span style='font-size:12.0pt;color:black'>shahid nayeem<br>
<br>
&nbsp;</span></font><font color=black><span style='color:black;mso-color-alt:
windowtext'><o:p></o:p></span></font></p>

<p class=MsoNormal style='margin-left:.5in'><span class=gmailquote><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>On 5/18/10, <b><span style='font-weight:bold'>Justin A. Lemkul</span></b>
&lt;<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>&gt; wrote:</span></font></span><font
color=black><span style='color:black'> </span></font><font color=black><span
style='color:black;mso-color-alt:windowtext'><o:p></o:p></span></font></p>

<div style='border:none;border-left:solid #CCCCCC .75pt;padding:0in 0in 0in 6.0pt'>

<p class=MsoNormal style='margin-left:40.8pt;border:none;mso-border-left-alt:
solid #CCCCCC .75pt;padding:0in;mso-padding-alt:0in 0in 0in 6.0pt'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'><br>
<br>
<span class=q>shahid nayeem wrote:</span></span></font><span class=q><font
color=black><span style='color:black;mso-color-alt:windowtext'><o:p></o:p></span></font></span></p>

</div>

<div style='border:none;border-left:solid #CCCCCC .75pt;padding:0in 0in 0in 6.0pt'>

<p class=MsoNormal style='margin-left:45.6pt;border:none;mso-border-left-alt:
solid #CCCCCC .75pt;padding:0in;mso-padding-alt:0in 0in 0in 6.0pt'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>Dear All<br>
I downloaded dsspcmbi.tar.gz, and compiled &nbsp;using command<br>
./DsspCompileGCC as given in Readme.txt file. when I try to run<br>
do_dssp command in gromacs I get error</span></font><font color=black><span
style='color:black;mso-color-alt:windowtext'><o:p></o:p></span></font></p>

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<p class=MsoNormal style='mso-margin-top-alt:0in;margin-right:0in;margin-bottom:
12.0pt;margin-left:40.8pt;border:none;mso-border-left-alt:solid #CCCCCC .75pt;
padding:0in;mso-padding-alt:0in 0in 0in 6.0pt'><font size=3 color=black
face="Times New Roman"><span style='font-size:12.0pt;color:black'><br>
Well, what happened?</span></font><span class=q><font color=black><span
style='color:black;mso-color-alt:windowtext'><o:p></o:p></span></font></span></p>

</div>

<div style='border:none;border-left:solid #CCCCCC .75pt;padding:0in 0in 0in 6.0pt'>

<p class=MsoNormal style='margin-left:45.6pt;border:none;mso-border-left-alt:
solid #CCCCCC .75pt;padding:0in;mso-padding-alt:0in 0in 0in 6.0pt'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'><br>
Fatal error:<br>
DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP)<br>
<br>
I checked for DSSP executible in /usr/local/bin/ and I couldnt find. I</span></font><font
color=black><span style='color:black;mso-color-alt:windowtext'><o:p></o:p></span></font></p>

</div>

<div style='border:none;border-left:solid #CCCCCC .75pt;padding:0in 0in 0in 6.0pt'>

<p class=MsoNormal style='mso-margin-top-alt:0in;margin-right:0in;margin-bottom:
12.0pt;margin-left:40.8pt;border:none;mso-border-left-alt:solid #CCCCCC .75pt;
padding:0in;mso-padding-alt:0in 0in 0in 6.0pt'><font size=3 color=black
face="Times New Roman"><span style='font-size:12.0pt;color:black'><br>
It won't be there unless you put it there and you have re-named it. &nbsp;I
believe the default name of the dssp program is &quot;dsspcmbi,&quot; which you
need to change when you move the executable.<br>
<br>
<a href="http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp"
target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp</a><br>
<br>
-Justin</span></font><span class=q><font color=black><span style='color:black;
mso-color-alt:windowtext'><o:p></o:p></span></font></span></p>

</div>

<div style='border:none;border-left:solid #CCCCCC .75pt;padding:0in 0in 0in 6.0pt'>

<p class=MsoNormal style='margin-left:45.6pt;border:none;mso-border-left-alt:
solid #CCCCCC .75pt;padding:0in;mso-padding-alt:0in 0in 0in 6.0pt'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>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</span></font><font color=black><span style='color:black;
mso-color-alt:windowtext'><o:p></o:p></span></font></p>

</div>

<div style='border:none;border-left:solid #CCCCCC .75pt;padding:0in 0in 0in 6.0pt'>

<p class=MsoNormal style='margin-left:40.8pt;border:none;mso-border-left-alt:
solid #CCCCCC .75pt;padding:0in;mso-padding-alt:0in 0in 0in 6.0pt'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'><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 href="http://vt.edu/" target="_blank"
onclick="return top.js.OpenExtLink(window,event,this)">vt.edu</a> | (540)
231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
<span class=sg>-- </span><br>
<span class=sg>gmx-users mailing list &nbsp; &nbsp;<a
href="mailto:gmx-users@gromacs.org" target="_blank"
onclick="return top.js.OpenExtLink(window,event,this)">gmx-users@gromacs.org</a></span><br>
<span class=sg><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">http://lists.gromacs.org/mailman/listinfo/gmx-users</a></span><br>
<span class=sg>Please search the archive at <a
href="http://www.gromacs.org/search" target="_blank"
onclick="return top.js.OpenExtLink(window,event,this)">http://www.gromacs.org/search</a>
before posting!</span><br>
<span class=sg>Please don't post (un)subscribe requests to the list. Use the
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org"
target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">gmx-users-request@gromacs.org</a>.</span><br>
<span class=sg>Can't post? Read <a
href="http://www.gromacs.org/mailing_lists/users.php" target="_blank"
onclick="return top.js.OpenExtLink(window,event,this)">http://www.gromacs.org/mailing_lists/users.php</a></span></span></font><font
color=black><span style='color:black;mso-color-alt:windowtext'><o:p></o:p></span></font></p>

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color=black><span style='color:black;mso-color-alt:windowtext'><o:p></o:p></span></font></p>

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