[gmx-users] grompp Unkown bond_atomtype C2

Lara Bunte lara.bunte at yahoo.de
Wed May 16 09:56:20 CEST 2012



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

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