Hi, Slipids are already compatible with Amber. Just download the proper lipid.itp file (DPPC.itp, DMPC.itp, ...) from the Slipids website, and include the below line in your .top after processing your protein with pdb2gmx (and selecting some Amber FF).
; Include lipid topology #include "./DMPC.itp" Of course, you can change the name of the lipid.itp according to the lipids in your system. The order in which this appears in your .top matters. If you add the lipids to your simulation box and then solvate it, the above line must come prior to the water.itp Regards, On 8/31/14, Yorquant Wang <wangy...@gmail.com> wrote: > Hi all, > I want to do a membrane protein simulation and I want to use amber FF > for protein (my target protein contains many beta sheet secondary > structures). But forcefield.ff file in the web: > http://people.su.se/~jjm/Stockholm_Lipids/Downloads.html, contains only > lipids parameter. I don't know how to conbined those lipid parameter > with amber99sb-ildn.ff. > Is there anybody who can help me? Thank you very much. > > > -- > Yukun Wang > PhD candidate > Institute of Natural Sciences && College of Life Science, Shanghai Jiao > Tong University > Cell phone: 13621806236. > China Shanghai > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. > -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.