Thank you so much for your information.its really help me a lot. On Sep 27, 2018 3:07 PM, "Peter Kroon" <p.c.kr...@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 <islamsha...@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.kr...@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-us...@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, <islamsha...@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-requ...@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-requ...@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-requ...@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-requ...@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-requ...@gromacs.org.