[gmx-users] secondary structure analysis

[P C Kroon]

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
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.