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
