Hi gromacs users: I am working on membrane peptides simulation under lipid (DPPC, from Peter Tieleman group site). I have downloaded the lipid and dppc .itp from the same site. The steps that I am following are as follows and all my files are in the work directory:
1)pdb2gmx_331 -f peptide_moved.pdb -o peptide_moved.gro -p peptide_moved.top -i peptide_moved_posre.itp -ff G53a5 -water spc -ter -lys -asp -glu -ignh 2)editconf_331 -f dppc64.pdb -o dppc64.gro (I changed DPPC x DPP and ATOM x HETATM) 3)cat peptide_moved.gro dppc64.gro > peptide_dppc64.gro (I've edited this file) 4)editconf_331 -f peptide_dppc64.gro -o peptide_dppc64_edit.gro (reorder the atoms) 5)editconf_331 -f peptide_dppc64_edit.gro -o peptide_dppc64_box.gro -bt triclinic -c -box 4.725 4.232 12 (Creating the water box) 6)genbox_331 -cp peptide_dppc64_edit_box.gro -cs -o peptide_dppc64_water.gro -p peptide_dppc64.top (add water molecules) But..when I run grompp 7)grompp_331 -f peptide_dppc64_em.mdp -po peptide_dppc64_em_out.mdp -c peptide_dppc64_water.gro -p peptide_dppc64.top -o peptide_dppc64_em.tpr It gives Fatal error: Invalid order for directive defaults, file ""lipid.itp"", line 8 this is my initial .top file ; Include forcefield parameters #include "ffG53a5.itp" ; Include chain topologies #include "peptide_moved.itp" #include "lipid.itp" #include "dppc.itp" ; Include water topology #include "spc.itp" #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 peptide StII-30 + dppc64 [ molecules ] ; name number Protein 1 DPP 64 SOL 5737 I haven't include the forcefield twice and my protein.itp hasn't it. I've done many things as suggested in mailing list that I explain in other mail cos i don´t send a message body bigger than 50Kb. Any help will be highly appreciated. Maite _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
