[gmx-users] Charge group problem from pdb2gmx
el.maestrox at gmail.com
Thu May 26 02:05:38 CEST 2011
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
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
Laboratorio de Biología Estructural y Molecular
Universidad de Chile
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