[gmx-users] topology

[Dayhoff, Guy]

On Feb 27, 2017, at 6:00 AM, gromacs.org_gmx-users-request at maillist.sys.kth.se<mailto:gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:

I am explaining my issues regarding complex simulation.

I have 200ns conformer(OPLS FF)

I have generated my ligand gro and itp file.(Using topolgen1_1)

I have edited my protein gro file and made it into complex file as per the
tutorials.

I have made changes to my topol.top file.

Now in my command for em.mdp I am getting 19 errors stating "NO DEFAULT
BOND TYPE, ANGLE TYPE, ETC.”


These errors are accompanied with line numbers pointing to the specific entry in your
topology file responsible for the respective errors.

Bonds, angles, dihedrals etc are all defined in the forcefield parameters. These errors
signify that there are entries in your topology file not found in the forcefield you’re using.

You should verify the topology file lines are error free and if so then you would work to
add the missing parameters to the forcefield to overcome the errors.

-Guy

Can you guide me with this?