[gmx-users] grompp error: Unknown bond_atomtype
vicolls at fizyka.umk.pl
vicolls at fizyka.umk.pl
Tue Mar 26 13:55:11 CET 2019
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
>> 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
> Where did I make mistake?
>> Have did you manage to add ligand topology?
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