[gmx-users] using martinize.py to martinize two chains complex

XAvier Periole x.periole at rug.nl
Thu Sep 6 00:52:23 CEST 2012

You may want to try the forum on rte cgmartini.nl for more ...

In short:

try "martinize.py -h" it should give you options to separate the chain  
topologies. If it does not work that means your chains are not defined  
as two in the input.

Their is not direct manner to CG a lipid file ... the topology is easy  
to build though ... for the coordinate files you either start from an  
already existing file or you go through the reverse transformation  
tutorial. It is mainly used to get atomistic from CG but you can do  
the inverse ... the steps are identical and most importantly you learn  
how to build a topology with  a "mapping" section.


On Sep 5, 2012, at 11:53 PM, Lingyun Wang wrote:

> Hi all,
> There are two chains in the complex.pdb file, but martinize.py only  
> recognize them as one chain. What can I do to generate two chains in  
> the complex-martini.top file? My command is as following:
> "python martinize.py  -f complex.pdb -o complex-martini.top -x  
> complex-martini.pdb"
> By the way, is any script to generate Martini topology and structure  
> files for lipids available? If not, how can I martinize a lipids  
> bilayer?. Thanks.
> Lingyun
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