[gmx-users] secondary structure analysis

P C Kroon p.c.kroon at rug.nl
Mon Sep 24 14:15:28 CEST 2018


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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