Dear all,
Message: 4
Date: Wed, 23 May 2007 10:16:59 -0400
From: Justin Lemkul <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] Re: Re: do_dssp for many peptides
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1
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.
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.
I saw a similar description in the archives a long time ago when I was looking
for help on do_dssp and experiencing similar problems (with a simpler system,
granted). Which group are you selecting for running do_dssp? These errors
seem to come up if you select any group other than 'MainChain' (choice 5, I
believe). If do_dssp is finding an incorrect number of "residues," perhaps you
have selected 'Protein' instead of 'MainChain' for your analysis?
Thanks for your reply, Justin. Indeed I had chosen 'Protein' so far. But
it is not evident that this caused the problem, since it worked well in
some cases. Indeed, choosing 'MainChain' (indeed index group 5) does not
help, but results in the same behavior.
Volker
--
Dr. Volker Knecht
Department of Theory and Bio-Systems
Max Planck Institute of Colloids and Interfaces
Research Campus Golm
14424 Potsdam, Germany
http://www.mpikg-golm.mpg.de/th/people/vknecht/index.html
Phone: +49-331-567-9610
Fax: +49-331-567-9612
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