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Dear all,<br>
<blockquote cite="mid20070523132910.65B5724086@xray.bmc.uu.se"
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<pre wrap="">Does anyone have an idea what is going wrong?
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No, but it would straightforward to write a script that used trjconv
while iterating through a set of index files that extract the
coordinates of just one peptide at a time, write that to an intermediate
.xtc file and send that to do_dssp individually. There's no chemical
reason to want do_dssp to do this looping for you, and you may discover
the source of the problem if/when this manual loop breaks.
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Thanks for your reply, Mark. As to the looping, I am actually
interested in *inter*molecular beta-sheets, so would have to do this
"external looping" over all pairs of peptides. I have tried to do a run
using an xtc and tpr file containing chains J and N described
previously, but I get into a similar trap as described in my previous
email (item 3). do_dssp claims
that are 248 residues in my selected group, although 248 is the number
of *atoms* (not of residues) of this peptide. After the notion that
some temporary file is backed up, do_dssp gets stuck again.<br>
<br>
I have even tried exactly Mark's suggestion (xtc file containing single
peptide) for test reasons, but a similar problem occurs for the peptide
denoted as chain N: do_dssp claims
that are 124 residues in my selected group, although 124 is the number
of *atoms* (not of residues) of this peptide. After the notion that
some temporary file is backed up, do_dssp gets stuck again.<br>
<br>
Volker<br>
<pre class="moz-signature" cols="72">--
Dr. Volker Knecht
Department of Theory and Bio-Systems
Max Planck Institute of Colloids and Interfaces
Research Campus Golm
14424 Potsdam, Germany
<a class="moz-txt-link-freetext" href="http://www.mpikg-golm.mpg.de/th/people/vknecht/index.html">http://www.mpikg-golm.mpg.de/th/people/vknecht/index.html</a>
Phone: +49-331-567-9610
Fax: +49-331-567-9612
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