Hi, The emails have been arriving, but you're asking a complicated series of questions. You need to find some literature that shows these protein and lipid force fields were parameterized in a compatible way, and even then you may need to show that you in fact get a physically reasonable result. Only once you've got that sorted does integrating details like the atom type descriptions into a hybrid forcefield folder become work worth doing. We haven't written code to make "combine two *.ff folders" work smoothly, because usually that's a nonsense operation...
Mark On Wed, Aug 23, 2017 at 3:07 PM Carlos Navarro <carlos.navarr...@gmail.com> wrote: > Dear gmx users, > > This is the third time I’m sending this email, but for some reason is not > been accepted. > > I’m trying to set up a system consisting in a protein embebed into a > bilayer. The whole system contains approximately ~400000 atoms, so to speed > up the simulation I'm using virtual sites. > > I had no issue by converting my initial structure (protein) into a .gro+vs > And for the lipid coordinates and parameters I’m using the one published in > the following article: > http://pubs.acs.org/doi/pdfplus/10.1021/acs.jctc.5b01202 files here-> > https://zenodo.org/record/47649#.WZssiHeGMcg (In the link are the > parameters for POPC, as well as the ffbonded and ffnonbonded for the slipid > forcefield). > > Unfortunately, since the lipids posses its own forcefield file (located in > slipids.ff) I don’t how how to include the parameters in the ‘main’ > topology file, because if I do add the slipid forcefield in I get the > following error: > > Fatal error: > > Syntax error - File forcefield.itp, line 5 > > Last line read: > > '1 2 yes 0.5000 0.8333' > > Found a second defaults directive. > > error, which make sense. > But also If I tried to add only the .itp file of POPCvs to the .top file > gromacs complain about the atomtypes: > > ERROR 1 [file POPCvs.itp, line 66]: > > Atomtype MCH3N not found > > > If I’m not mistaken, I have read some articles were people indeed can > combine different forcefield, but sadly I don’t know how to do that. > If this is imposible to do, does someone know vsite parameters for POPC > that can be use in charmm36? > Hope someone can help me. > Best regards, > Carlos > -- > 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. -- 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.