[gmx-users] do_dssp for many peptides

Mark Abraham Mark.Abraham at anu.edu.au
Wed May 23 14:50:41 CEST 2007

Volker Knecht wrote:
> 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.


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