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

[shivangi nangia]

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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