[gmx-users] CG-MD to study the conformational changes of proteins...
Shanmuga Priya V.G
priyaabhirajan at gmail.com
Mon Dec 26 20:15:19 CET 2016
Dear Gromacs Users,
I have a insilico model of Mycobacterium cell wall (surface) protein
which has no transmembrane helices.Which Gromacs tutorials should I
follow for MD studies to know about its conformational stability and
latter for protein - ligand studies. Kindly guide me
On Mon, Dec 26, 2016 at 11:06 PM, Dariush Mohammadyani <
d.mohammadyani at gmail.com> wrote:
> Hi Quyen,
> Although Martini is a good CG force field for a system contains lipids and
> proteins, it still needs some improvements to capture conformational
> changes (especially large changes).
> Is there any hybrid model available (and ready to use) for such a system?
> On Mon, Dec 26, 2016 at 11:23 AM, Quyen V. Vu <vuqv.phys at gmail.com> wrote:
> > Nikhil say:
> > I would like to study the conformational study of proteins (Amyloid beta)
> > in presence of lipid bilayers and other molecules. Can anyone tell me the
> > possibility of Coarse-grained molecular dynamics for this study, since
> > all-atom MD need more time and my system contains more atoms, so I'm
> > thinking to go for CGMD. in CG-MD can we do the same analysis as in
> > All-atom MD.?
> > You need to find a force field that support for protein coarse-grain
> > such as Martini: http://cgmartini.nl/
> > to save simulation time you can you CG model or hybrid model( result
> > better than CG model because a important region
> > is treated as standard MD, less important region is use CG model
> > --
> > 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.
More information about the gromacs.org_gmx-users