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

[shivangi nangia]

Thanks Tsjerk.
On Nov 12, 2014 3:27 PM, "Tsjerk Wassenaar" <tsjerkw at gmail.com> wrote:

> 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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