[gmx-users] generating martini-version of lipids

[Tsjerk Wassenaar]

Hi Jagannath,

Have a look at the mappings for dppc and popg. It's quite easy to create
the one for popg. If you only want to do forward mapping it is sufficient
to list one corresponding CG bead for each atom.

Cheers,

Tsjerk
On Mar 1, 2016 07:41, "jagannath mondal" <jm3745 at columbia.edu> wrote:

> Hi Tsjerk
>   Thanks for your response. I was mainly looking for converting a dppg
> bilayer in charm36 format into a coarse-grained one. However, the "Mapping"
> folder does not have any mapping for dppg lipids. Is there any specific
> suggestion regarding this?
> Jagannath
>
> On Mon, Feb 29, 2016 at 10:10 PM, Tsjerk Wassenaar <tsjerkw at gmail.com>
> wrote:
>
> > Hi Jagannath,
> >
> > Backward actually can do both. For conversion of a Gromos system use
> >
> > backward.py -from gromos -to martini
> >
> > Hope it helps,
> >
> > Tsjerk
> >
> >
> > On Mon, Feb 29, 2016 at 11:20 AM, Jagannath Mondal <
> > jmondal.backup at gmail.com
> > > wrote:
> >
> > > Dear Gromacs/Martini-users
> > >
> > > I wanted to transform a snapshot of my atomistic DPPG/water bilayer to
> > the
> > > Martini coarse-grained format. However, I found martinize.py script
> does
> > > not transform lipid or waters to coarse-grained counterpart.It only
> works
> > > for protein. So, Is there any particular way I can generate the CG
> > version
> > > of my atomistic DPPG/water bilayer ?
> > >
> > > I guess backward scripts does the reverse of what I am trying to
> achieve.
> > > So, if you can suggest a way to generate a coarse-grained pdb files of
> > the
> > > atomistic lipid bilayer/water, that will be very helpful.
> > >
> > > Jagannath
> > > --
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> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> > --
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