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

[shivangi nangia]

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