[gmx-users] grompp error: Unknown bond_atomtype

[vicolls at fizyka.umk.pl]

Cytowanie RAHUL SURESH <drrahulsuresh at gmail.com>:

> On Tue 26 Mar, 2019, 6:18 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 ..

I just download PDB file with membrane cluster structure from  
charmm-gui. No topology, no parameters at all. Only coordinates. Then  
I found parameters in amber force field for this DLPC and proceeded  
both pdb structure and parameters .itp with pdb2gmx. Everything  
worked.  But now got troubles with energy minimization/simulations.

>> >>
>> >
>> >>
>> >
>> >
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>>
>>
>>
>