Cytowanie RAHUL SURESH <drrahulsur...@gmail.com>:
On Tue 26 Mar, 2019, 6:00 PM , <vico...@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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