[gmx-users] secondary structure analysis

[SHAHEE ISLAM]

Thank you so much for your information.its really help me a lot.

On Sep 27, 2018 3:07 PM, "Peter Kroon" <p.c.kroon at rug.nl> wrote:

> No, this is not correct.
>
> Prehaps I worded my first e-mail too subtly. The secondary structure of
> a protein in a normal Martini simulation *will not* change. Trying all
> sorts of tricks to make the analysis program happy will not change this.
> The secondary structure is fixed by your topology. Either through
> elastic bonds, or through extended dihedrals.
>
> If you do see a difference in SS between the start and end of your
> simulation either a) you did something wrong or b) your looking at an
> analysis artefact.
>
> Martini is not the right tool to study SS changes.
>
> Peter
>
>
> On 25-09-18 09:13, SHAHEE ISLAM wrote:
> > by using only the .gro is it possible to calculate the secondary
> > structure of protein.because when i am using this comment
> > do_dssp -s aa_charmm-eq.gro -n ../index-p.ndx -sss scount-p-0-1.xvg -o
> > ss-p-0-1.xpm
> > the error is
> > Can not open file:
> > traj.xtc
> > because i have the all atom gro file (obtained by converting cg.gro to
> > all atom gro file.) i cant use the .xtc file ,because it is a martini
> > cg.xtc file.
> > thanking you
> > shahee
> >
> > On 9/24/18, SHAHEE ISLAM <islamshahee at gmail.com> wrote:
> >> thank you so much for your quick reply.if i convert the coarse grained
> >> pdb into all atom gro file,then vmd can calculate the secondary
> >> structure.is this correct or there are other way to calculate the
> >> change of secondary structure of protein.
> >>
> >> On 9/24/18, P C Kroon <p.c.kroon at rug.nl> wrote:
> >>> Hi Soham,
> >>>
> >>> In normal Martini you *can NOT* see secondary structure changes. It is
> >>> usually fixed using either elastic bonds or extended dihedrals. If you
> >>> apply
> >>> neither it will generally collapse into a spherical ball of entropy.
> >>> Please
> >>> refer to e.g. Monticelli et al. [1]
> >>> Also, in general, analysis tool (VMD, DSSP) don’t like CG structures.
> >>> They
> >>> don’t recognise the names of the particles (and to be honest, I don’t
> >>> blame
> >>> them)
> >>>
> >>> Peter
> >>>
> >>> [1] L. Monticelli, S. K. Kandasamy, X. Periole, R. G. Larson, D. P.
> >>> Tieleman, S. J. Marrink, J. Chem. Theory Comput., 2008,
> >>> DOI:10.1021/ct700324x.
> >>>
> >>> From: Soham Sarkar
> >>> Sent: 24 September 2018 14:10
> >>> To: gmx-users at gromacs.org
> >>> Subject: Re: [gmx-users] secondary structure analysis
> >>>
> >>> You can use do_dssp utility to generate the secondary structure
> >>>
> >>> On Mon, 24 Sep 2018, 5:34 pm SHAHEE ISLAM, <islamshahee at gmail.com>
> wrote:
> >>>
> >>>> hi,
> >>>> i am doing martini based coarsed coarse grained simulation in
> >>>> gromacs.after getting the coarse grained structure ,i can convert cg
> >>>> pdb it to the gro file.using vmd, seondary structure can be
> >>>> analysed.can any one suggest what may be the best way to calculate the
> >>>> secondary structure change of protein.
> >>>> thanking you
> >>>> shahee
> >>>> --
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