[gmx-users] do_dssp: main chain

[Volker Knecht]

Dear all,

>Message: 4
>Date: Wed, 23 May 2007 10:16:59 -0400
>From: Justin Lemkul <jalemkul at vt.edu>
>Subject: Re: [gmx-users] Re: Re: do_dssp for many peptides
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <1179929819.46544cdb08c4f at webmail.vt.edu>
>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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