[gmx-users] grompp error: Unknown bond_atomtype

Justin Lemkul jalemkul at vt.edu
Tue Mar 26 14:36:09 CET 2019

On 3/26/19 8:22 AM, 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.
> Where did I make mistake?
It looks like you're mixing force fields between AMBER and CHARMM. CTL3 
is a CHARMM atom type. You cannot mix force fields; you must develop the 
topology under a single, consistent parameter set.



Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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