[gmx-users] protein-ligand simulation problem

[Prabir Khatua]

Hi Gromacs Users,

I am trying to protein-ligand simulation where I have 12 protein and 12
ligand molecules.
Minimization step went perfectly well and the system got minimized less
than 20000 steps.
However, it is becoming unstable once I am trying to do real simulation. I
am trying to equilibrate the system by applying restraints on protein and
ligand separately with two tc_groups (protein_ligand and water_ions) in NVT
ensemble. The following error I am receiving

WARNING: Listed nonbonded interaction between particles 210 and 214
at distance 42.035 which is larger than the table limit 2.001 nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.

I cannot understand why such a problem is arising while the minimization
went well. Thus,
I would expect the system not to have bad contacts. On visualizing the
system in VMD, I did
not see any significant bad contacts. Can you please help me to fix this
issue?
Is there any way to minimize the system in a better way to avoid bad
contacts, if any?

Thanks in advance,

Prabir

-- 

*Prabir Khatua*
*Postdoctoral Research Associate*
*Department of Chemistry & Biochemistry*
*University of Oklahoma*
*Norman, Oklahoma 73019*
*U. S. A.*