Hi everyone. I am a relatively new user of GROMACS having recently needed to carry out research on proteins aggregation.
I am currently building a DMPC/DMPG 1:1 membrane by assembling individual DMPC and DMPG lipid molecules and then using genconf to generate the amount of lipids needed. The DMPC topology was taken from Dr. Tielman website, while DMPG was taken from lipidbook. Now I am facing issue as to how to I make the topologies for the 2 different lipids compatible with each other. The DMPC topology is compatible with gromos combined with Berger lipid parameter, while the DMPG was done with 54A7. I would like to use 54A7 without Berger lipid parameters, what would be the best way to do it? Modifying the residue name? If so, do I only have to modify the topology dmpc.itp that comes from Dr. Tielman website, such that the residue name follows the 54A7 convention? The reason I want to use the lipid without Berger lipid is that there's a recent paper http://pubs.acs.org/doi/abs/10.1021/ct300675z that suggests that 54A7 is the better united atom FF as compared to the other FF commonly used, including the Berger Gromos combination. What is your opinion? Best Regards, Khi Pin -- View this message in context: http://gromacs.5086.x6.nabble.com/Building-lipid-bilayers-topology-tp5011774.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
