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

[Adriana Garro]

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
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>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
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