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

[Lingyun Wang]

Hi XAvier,

Thank you for your reply. 
I also tried " python martinize.py  -f complex.pdb -o complex-martini.top -x complex-martini.pdb -sep", but it still turns out the same result. There is "Ter" after each chain in the pdb, do I need other way to define that they are two chains? Thanks.

Best,
Lingyun 
________________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of XAvier Periole [x.periole at rug.nl]
Sent: Wednesday, September 05, 2012 5:52 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] using martinize.py to martinize two chains complex

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.

XAvier.

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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