[gmx-users] secondary structure analysis

[SHAHEE ISLAM]

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
>> --
>> 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.
>
> --
> 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.