[gmx-users] Re: Re: do_dssp for many peptides

[Volker Knecht]

Dear all,

>>Does anyone have an idea what is going wrong?
>>    
>>
>
>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.
>  
>
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.

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.

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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