Hi KT, Either way should be fine. g_membed is not linked to a specific force field, so you can use it for coarse grained models too. You can also first set up an AA model and convert to CG afterwards. However, martinize.py only works for the protein, so you have to convert the lipids in a different way.
Cheers, Tsjerk On Thu, Dec 27, 2012 at 2:00 AM, Kieu Thu Nguyen <[email protected]>wrote: > Dear All, > > When using g_membed tool to embed protein into membrane, can i use Martini > forcefield to generate the topology file ? > > Or can i use the all-atom forcefield to generate the .top file, and after > protein have inserted, AA representation have converted into CG > representation by using martinize.py ? > > Thank for any advice ! > Best regards, > KT > -- > gmx-users mailing list [email protected] > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
