Hi After:
pdb2gmx -f mymol.pdb -water tip3p editconf -f conf.gro -bt dodecahedron -d 1.3 -o box.gro genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro I typed: grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr where em.mdp is my energy minimization file and I got: Fatal error: Unknown bond_atomtype C2 What is here the problem? All atom types should be declared by me, I guess. Thanks for helping me Greetings Lara -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
