[gmx-users] grompp error: Unknown bond_atomtype

RAHUL SURESH drrahulsuresh at gmail.com
Tue Mar 26 13:36:30 CET 2019

On Tue 26 Mar, 2019, 6:00 PM , <vicolls at fizyka.umk.pl> wrote:

> Hello everyone,
> I would call myself newbie gromacs user and need some help with task
> that was given to me. I'm supposed to take protein-ligand complex
> (bounded by covalence bond) and put it  into membrane. I'm glad I've
> created the complex in amber force field. But now I stucked around
> membrane think.
> I have created DLPC-only membrane cluster in charmm-gui. I have found
> parameters for this type of lipid. I did add additional names for atom
>   in  atomtypes.atp, include ffbonded_lipid.itp and
> ffnonbonded_lipit.itp files to forcefrield.itp and put into amber
> forcefield directory t he lipids.rtp file. Gladly  everything went
> smoothly with pdb2gmx  with my membrane. I get topol.top file. Then I
> wanted to try minimize energy. I've prepared .mdp file and used gromp
> with:
> gmx grompp -f minim.mdp -c membrane_solv.gro -p topol.top -o em.tpr
> Unexpectedly I get error "Unknown bond_atomtype CTL3", though CTL3 is
> defined in atomtypes.atp  and the bond have its parameters inside the
> ffbond.itp file. It's really strange for me, beacuse I thought that if
> topol.top file was created there is no possibility to get some
> troubles with defined atoms, bonds, etc.
> This CTL3 is that of ligand?

Where did I make mistake?
> Have did you manage to add ligand topology?

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