Im working on simulating a CYP2D6 with its cofactors (heme ) with GROMACS. When I run pdb2gmx, using CHARMM27 FF, I had no error. After looking in the literature, I found their corresponding parameters: I added the following fields in CHARMM file ffbonded.itp [ bondtypes ] ; i j func b0 kb SG FE 1 0.232 209200.0
[ angletypes ] ; i j k func th0 cth ub0 cub CT2 SG FE 5 100.6 418.4 0.0 0.0 SG FE NPH 5 90.0 836.8 0.0 0.0 SG FE NPH 5 90.0 836.8 0.0 0.0 SG FE NPH 5 90.0 836.8 0.0 0.0 SG FE NPH 5 90.0 836.8 0.0 0.0 ; ### X CS SS X 9 0.20 0.0 3 CA CB SG FE 9 0.20 0.0 3 HB1 CB SG FE 9 0.20 0.0 3 HB1 CB SG FE 9 0.20 0.0 3 ; ### X FE SS X 9 0.00 0.0 4 CB SG FE NPH 9 0.00 0.0 4 CB SG FE NPH 9 0.00 0.0 4 CB SG FE NPH 9 0.00 0.0 4 But after that, I had another type of error: Fatal error: Unknown bond_atomtype SG, I correct it by default. after that in grompp step : I got error ERROR 7 [file topol.top, line 41571]: > No default Proper Dih. types > > Fatal error: > There were 24 errors in input file(s). what should I do? > -- 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.
