[gmx-users] Charge group problem from pdb2gmx

[Felipe Villanelo]

Hi everybody

I want to run a EM, but grompp give me this Note:

  The sum of the two largest charge group radii (0.305345) is larger than
  rlist (1.000000) - rvdw (0.900000)

I have read in the gmx forums, that this is a problem from the designation
of charge groups, but I have make the topology with Gromacs pdb2gmx and
there is no other molecule, different of protein with standard residues.
Even if I try to run the EM just with the protein in vacuum, the error is
the same.

So the problem cames from pdb2gmx which is not making the correct charge
groups assignation from a simple protein.

But when I use the AMBER ff, this problem dissapear. However, I need to use
the GROMOS96 ff (In the future, I want to simulate the protein with a ligand
parametrizied with this ff)

I could try to change the rlist/rcoulomb and rvdw, but I think that this is
not a real solution.

Txn for the help


Felipe Villanelo Lizana
Bioquímico
Laboratorio de Biología Estructural y Molecular
Universidad de Chile
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