[gmx-users] Secondary Structure Restraints: martinize.py

Tsjerk Wassenaar tsjerkw at gmail.com
Fri May 1 21:59:54 CEST 2015

Hi sxn,

What do you mean with reverse coarse graining?
You can specify the secondary structure also as string, which is doable if
the peptide is not too long, e.g. using -ss HHHHHHHLLLLLLL. Otherwise, you
can put the secondary structure you want in a simple file, and pass that
with the option -ss.



On Fri, May 1, 2015 at 4:24 PM, shivangi nangia <shivangi.nangia at gmail.com>

> Hello,
> I wish to turn off the secondary structure restraint in half of the peptide
> while using martinze.py.
> Is there any way in which this can be done.
> I have tried to delete the columns in .dssp file which tell about the
> structure and character of the peptide but I still get a completely helical
> peptide on reverse coarse graining.
> Thanks in advance.
> Best,
> sxn
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Tsjerk A. Wassenaar, Ph.D.

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