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

[Tsjerk Wassenaar]

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,

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

> 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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