Dear all, I'm trying to simulate several drug-protein complexes on a clustered server. I used PRODRG and editted my .top, .pdb, .gro and posre.itp files. Here is the final lines of my .top file:
; Include Position restraint file ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif ; Include water topology #include "spc.itp" ; Include Dio topology #include "dio.top" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include generic topology for ions #include "ions.itp" [ system ] ; Name Nona in water [ molecules ] ; Compound #mols Protein_X 1 Dio 1 SOL 63598 The statements are closed with #endif. Yet I recieve "No molecules were defined in the system". For the same file I sometimes get "No such molecule type Dio" in the first grompp prompt. What's the solution? Regards, Sarah Keshavarz -- 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
