[gmx-users] grompp error: Unknown bond_atomtype

[RAHUL SURESH]

On Tue 26 Mar, 2019, 6:18 PM , <vicolls at fizyka.umk.pl> wrote:

> Cytowanie RAHUL SURESH <drrahulsuresh at gmail.com>:
>
> > 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?
>
> No, I'm  doing right now ONLY membrane. There are only lipids in the
> .gro file with solvataion and the CTL3 is atom of lipid. I just wanted
> to check if I'm able to create membrane-only system first.  If
> everything will work I'll  try  to embed protein+ligand in  this
> membrane.
>
> If I believe you are using amber ff for the lipids generated using charm
> GUI, then I should say the nomenclature of the lipid membrane will be in
> charmm format. Either you must use charmm ff or you have to use lipids for
> amber ff ..
> >>
> >
> > Where did I make mistake?
> >>
> >> Have did you manage to add ligand topology?
> >>
> >
> >
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