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.