OK. Thanks a lot justin<br><br><div class="gmail_quote">On Tue, Aug 18, 2009 at 1:16 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div class="im"><br>
<br>
sunny mishra wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Justin,<br>
<br>
Thanks for the expedient reply. So in that case I cannot get the dssp output of my CG structure for sure. So in that case do I have to get the .ssd files of my 1K4C_clean.pdb file only right and then get the .seq file of 1K4c_clean.pdb in order to proceed. Am I right?<br>
<br>
</blockquote>
<br></div>
Right, to generate the MARTINI topology you need both .ssd and .seq files.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Sunny<div><div></div><div class="h5"><br>
<br>
On Tue, Aug 18, 2009 at 1:03 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
sunny mishra wrote:<br>
<br>
Dear all,<br>
<br>
I wanted to get the dssp output of Coarse Grained structure of<br>
my protein i.e. 1K4C. In order to get that I have a script which<br>
is given to me in the MARTINI tutorial (dssp2ssd.py). I have<br>
also downloaded the dssp successfully in my linux machine. In my<br>
first step i cleaned the 1K4C protein and renamed it as<br>
1K4C_clean.pdb. 1K4C_clean.pdb consists only the header title<br>
and atoms with C ligands in it. When i convert the<br>
1K4C_clean.pdb to CG structure using atom2CG script with the<br>
help of awk command I get the CG structure successfully and I<br>
renamed it 1K4C_cleancg.pdb. But when I am trying to get the<br>
dssp output of 1K4C_cleancg.pdb using dssp it produces nothing<br>
but on the other hand it produces the dssp output of my normal<br>
cleaned 1K4C pdb file. Do you know if there is anyway I can get<br>
the dssp output of my CG structure of protein?<br>
<br>
<br>
Not likely. DSSP calculates secondary structure from hydrogen<br>
bonds, which will be absent in a CG model. The script you refer to<br>
(dssp2ssd.py) does not use DSSP to calculate secondary structure; it<br>
simply converts DSSP output to the .ssd file needed by MARTINI.<br>
<br>
-Justin<br>
<br>
Thanks,<br>
<br>
Sunny<br>
<br>
<br>
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-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="im"><br>
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</div></blockquote><div><div></div><div class="h5">
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a 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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