[gmx-users] build itp file using martinize.py

[Tsjerk Wassenaar]

Hi Adriana,

I'm not aware of such a program. It will be kind of hard for Martini, as
the topology depends on the secondary structure. The only way I could think
of is to backmap the CG structure and then forward map again using
martinize.

Cheers,

Tsjerk

On Fri, Oct 31, 2014 at 1:30 PM, Adriana Garro <adrianagarrosl at gmail.com>
wrote:

> Hi Tsjerk,
>
> Thanks for your time.
> Sorry for the delay to answer but I was doing some tests...
> by the way, there is a program to generate a topology for a coarse grained
> structure?
> Thanks
>
> Adriana
>
>
>
> ***********************************************************
> Dra. Adriana D. Garro
> Química Medicinal
> Facultad de Química, Bioquímica y Farmacia
> Universidad Nacional de San Luis
> IMASL-CONICET
> San Luis, Argentina
>
> Tel..............:+54 266 4424689 int 6153
> e-mail...: adgarro at unsl.edu.ar
> e-mail...:  adrianagarrosl at gmail.com
>
>
> **********************************************************
>
> 2014-10-29 22:59 GMT+01:00 Tsjerk Wassenaar <tsjerkw at gmail.com>:
>
> > Hi Adriana,
> >
> > martinize is written to coarse grain proteins (and nucleic acids). It
> just
> > can't generate a topology for coarse grained structure, which is a quite
> > different problem. I'm also not exactly sure what increasing by one
> 'unit'
> > means. One residue, one molecule, one copy of a system? If it's about
> > adding molecules, you can simply use the itp for one unit and specify in
> > the .top file you'll have more of that molecule. If it's something else
> you
> > need, please be more specific about what you're trying to do.
> >
> > Cheers,
> >
> > Tsjerk
> >
> > On Wed, Oct 29, 2014 at 3:42 PM, Adriana Garro <adrianagarrosl at gmail.com
> >
> > wrote:
> >
> > > Dear gromacs users,
> > >
> > > I am working on a system which is builded step by step so I use the
> > output
> > > file like input file in the next simulation, I am trying to build a
> > stack;
> > > it is coarse grained combined with TMD. I want to create a topology
> (itp
> > > file) from a coordinate file (gro file) but when I try to run
> > martinize.py
> > > it gives me an error because the gro file is already coarse grained.
> how
> > > can I create the topology of my new system which has been increased in
> > one
> > > "unit"?
> > > I would really appreciate some help, I can provide more information if
> it
> > > is not clear.
> > > Thanks in advance!
> > > Cheers
> > >
> > > Adriana
> > > --
> > > 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.
> > >
> >
> >
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> > --
> > 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.
>



-- 
Tsjerk A. Wassenaar, Ph.D.