All right, I see. Thank you. 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 6:47 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] using martinize.py to martinize two chains complex
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 -- 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
