Dear Justin Very thanks for your reply.
I created a new topol.top file as below: 1) I used once default directive. 2) I put cnt.itp file in working directory. 3) I copied pr.top and renamed it to topol.top. I added #include "cnt.itp" in the end of topol.top file. I modified [ molecules ] directive. ------------------------------------------------------------------------------------------ begining of topol.top file is as follows: ; Include forcefield parameters #include "charmm27.ff/forcefield.itp" [ moleculetype ] ; Name nrexcl Protein_chain_A 3 [ atoms ] . . . . end of com.top file is as follows: ; Include Position restraint file #ifdef POSRES #include "posre.itp" #endif #include "cnt.itp" ; Include water topology #include "charmm27.ff/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include "charmm27.ff/ions.itp" [ system ] ; Name Protein in water [ molecules ] ; Compound #mols Protein_chain_A 1 CNT 1 SOL 1388 ------------------------------------------------------------------------------------------- Previous error (Invalid order for directive defaults) was solved, but When I used grompp -f minim.mdp -c system.gro -p topol.top -o minim.tpr, I encountered with this error: ERROR 1 [file cnt.itp, line 2861]: No default Angle types . . . . . . ERROR 1218 [file cnt.itp, line 4078]: No default Angle types Fatal error: There were 1218 errors in input file(s). Lines 2861-4078 are related to [ angles ] directive in cnt.itp file. -------------------------------------------------------------------------------- How to solve this issue? Any help will highly appreciated. -- 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