Ok now after downloading the latest version of dssp, and giving right permissions and after executing the /usr/local/bin/dssp command I am getting the following output :-<br><br>[root@BHARATPC peptide2]# /usr/local/bin/dssp <br>
DSSP options:<br> -h [ --help ] Display help message<br> -i [ --input ] arg Input file<br> -o [ --output ] arg Output file, use 'stdout' to output to screen<br> -v [ --verbose ] Verbose output<br>
-d [ --debug ] arg Debug level (for even more verbose output)<br><br><br>Examples: <br><br>To calculate the secondary structure for the file 1crn.pdb and<br>write the result to a file called 1crn.dssp, you type:<br><br>
dssp.exe -i 1crn.pdb -o 1crn.dssp<br><br><br><br><div class="gmail_quote">On Thu, Apr 5, 2012 at 4:23 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"><div class="im">
On 5/04/2012 5:16 PM, bharat gupta wrote:
</div><div class="im"><blockquote type="cite"><i>This is the output :<br>
<br>
[root@BHARATPC ~]# /usr/local/bin/dssp<br>
</i></blockquote>
<br></div>
Don't run as root except for installing software, unless you like
rebuilding your computer from the ground up.<br>
<br>
<blockquote type="cite"><i>bash: /usr/local/bin/dssp: Permission denied<br>
</i></blockquote>
<br>
Possibly you didn't give execute permission on some file or other.
This is not a GROMACS problem, but rather a problem with how you
have done your dssp installation. Consult its documentation.<div class="im"><br>
<br>
<blockquote type="cite"><i><br>
I have already set the pat for dssp in .bashrc using export
command , I don't know why this error is there. Is it due to
renaming dsspcmbi to dssp ??<br>
</i></blockquote>
<br></div>
You have now reported testing a command different from the one you
reported that you had instructed do_dssp to use. So it is hard for
me to believe your assertion that you are following the advice in
do_dssp -h correctly with a correct version of DSSP.<div><div class="h5"><br>
<br>
Mark<br>
<br>
<blockquote type="cite"><i>
</i><br>
<br>
<div class="gmail_quote">On Thu, Apr 5, 2012 at 4:08 PM, Mark
Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div> On 5/04/2012 4:16 PM, bharat gupta wrote:
<blockquote type="cite">Yes , I am using the correct
options for dssp. But still I am getting the same error.
<br>
</blockquote>
<br>
</div>
What does invoking /usr/local/bin/dsspcmbi say?<span><font color="#888888"><br>
<br>
Mark</font></span>
<div>
<div><br>
<br>
<blockquote type="cite"><br>
<div class="gmail_quote">On Thu, Apr 5, 2012 at 2:12
PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<div>On 5/04/2012 10:25 AM, bharat gupta wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"> Hi,<br>
<br>
I am trying to plot the ss content using the
do_dssp command , but I am getting the
following error :-<br>
<br>
Failed to execute command:
/usr/local/bin/dsspcmbi -na ddldj5Bn
ddXN9mH0 > /dev/null 2> /dev/null<br>
<br>
I am using the DSSPold version. What could
be the possible reason for such an error ??<br>
</blockquote>
<br>
</div>
</div>
Many of them. Start by making sure you're
following the advice of do_dssp -h.<span><font color="#888888"><br>
<br>
Mark</font></span>
<div>
<div><br>
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Room No. : 7202A, 2nd Floor<br>
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Ph.D. Candidate<br>
Room No. : 7202A, 2nd Floor<br>
Biomolecular Engineering Laboratory<br>
Division of Chemical Engineering and Polymer Science<br>
Pusan National University<br>
Busan -609735<br>
South Korea<br>
Lab phone no. - +82-51-510-3680, +82-51-583-8343
<div>
Mobile no. - 010-5818-3680<br>
E-mail : <a href="mailto:monu46010@yahoo.com" target="_blank">monu46010@yahoo.com</a></div>
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Room No. : 7202A, 2nd Floor<br>Biomolecular Engineering Laboratory<br>Division of Chemical Engineering and Polymer Science<br>Pusan National University<br>Busan -609735<br>South Korea<br>Lab phone no. - +82-51-510-3680, +82-51-583-8343<div>
Mobile no. - 010-5818-3680<br>E-mail : <a href="mailto:monu46010@yahoo.com" target="_blank">monu46010@yahoo.com</a></div><br>