On 5/16/12 3:56 AM, Lara Bunte wrote:
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.
You're making use of an atom type called "C2" in some bonded interaction, but
such an atom type doesn't exist. You need to define it.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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