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?
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