[gmx-users] secondary structure analysis

[Peter Kroon]

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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