[gmx-users] Apply secondary structure restraints only on part of the peptide while coarse graining

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Nov 12 21:26:51 CET 2014

Hi sxn,

You can supply a secondary structure string with the option -ss. That may
also be provided as a file. you can also just modify the residues you need
to have different in the dssp output. Only the actual classification string
is used.

Hope it helps,

On Nov 12, 2014 4:00 PM, "shivangi nangia" <shivangi.nangia at gmail.com>

> Hello Dear GMX users,
> I want to apply secondary structure constraints only on a part of my
> peptide while coarse graining (martinize.py), which contains a helical part
> and the rest of the structure is disordered.
> If  I supply a .dssp file only of part of the peptide, I only get the first
> coarse grained part of the peptide back.
> Is there a way around this?
> Kindly suggest.
> Thanks,
> sxn
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