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

[shivangi nangia]

Hello Tsjerk,


I am executing the following command to get half helical and half random cg
structure

The pdb I am supplying is a helical peptide

./martinize.py -f gamma1_unmutated.pdb -x gamma1_unmutated.elnedyn.pdb -o
gamma1.elnedyn.top  -ss LLLLLLLLLLHHHHHHHHHHH -p backbone  -ff martini22 >
 martinize.out

Then I minimize and rebox this cg peptide and reverse cg

./my_intiram.sh -f ../elnedynoff/reboxed_min_gamma1.gro -p protein_aa.top
-po prot_bkmapped.top -from martini -to charmm36

The backmapped.gro I get is not half random/half helical.

Is there anything that I am doing wrong?

Kindly guide.

Thanks,
sxn

On Fri, May 1, 2015 at 4:43 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> 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.
> --
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