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-boun...@gromacs.org [gmx-users-boun...@gromacs.org]
on behalf of XAvier Periole [x.peri...@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
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search
before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search
before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search
before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
