[gmx-users] Re: Re: do_dssp for many peptides
vknecht at mpikg.mpg.de
Wed May 23 15:55:45 CEST 2007
>>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.
Dr. Volker Knecht
Department of Theory and Bio-Systems
Max Planck Institute of Colloids and Interfaces
Research Campus Golm
14424 Potsdam, Germany
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