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

[XAvier Periole]

I believe martinize looks for chain identifiers. There is a column for  
that in the PDB format.

The other solution is to proceed in two steps ... one chain at the  
time ...

On Sep 6, 2012, at 1:22 AM, Lingyun Wang wrote:

> 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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