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

[Tsjerk Wassenaar]

Hi sxn,

With martinize.py -ss LLLLLLLLLLLHHHHHHHHHH
you'll get the secondary structure you want.

Cheers,

Tsjerk

On Fri, May 1, 2015 at 10:24 PM, shivangi nangia <shivangi.nangia at gmail.com>
wrote:

> Hello Tsjerk,
>
> Thanks for the reply.
>
> I have a 21 amino acids helical peptide, I want to first 10 amino acids to
> not having secondary structure restraints while coarse graining using
> martinize.py and the rest to remain helical.
>
> I reverse coarse the peptide to see if my trials while playing around with
> different trials with secondary structure file (I provide with -ss) changes
> worked or not. For example, in one of my trials I changed the structure
> column of the .dssp file from H to nothing hoping once I coarse grain with
> that modified file I would get a semi secondary structure restrained coarse
> grained peptide.
>
> Thanks,
>
> sxn
>
> On Fri, May 1, 2015 at 3:59 PM, Tsjerk Wassenaar <tsjerkw at gmail.com>
> wrote:
>
> > 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.
> >
> > Cheers,
> >
> > Tsjerk
> >
> >
> > On Fri, May 1, 2015 at 4:24 PM, shivangi nangia <
> shivangi.nangia at gmail.com
> > >
> > wrote:
> >
> > > 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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-- 
Tsjerk A. Wassenaar, Ph.D.