[gmx-users] grompp error: Unknown bond_atomtype

vicolls at fizyka.umk.pl vicolls at fizyka.umk.pl
Tue Mar 26 13:30:11 CET 2019

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  

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.

Where did I make mistake?

More information about the gromacs.org_gmx-users mailing list