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

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Oct 29 22:59:27 CET 2014

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.



On Wed, Oct 29, 2014 at 3:42 PM, Adriana Garro <adrianagarrosl at gmail.com>

> 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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