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

[Tsjerk Wassenaar]

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.