[gmx-users] grompp error: Unknown bond_atomtype

[vicolls at fizyka.umk.pl]

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.

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