[gmx-users] Charge group problem from pdb2gmx

Justin A. Lemkul jalemkul at vt.edu
Thu May 26 02:10:55 CEST 2011

Felipe Villanelo wrote:
> 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.

The problem does not come from pdb2gmx; it comes from your .mdp file.  The 
settings specified are incorrect for Gromos96 force fields.  For Amber, you 
receive no error because all charge groups consist of only one atom, 
essentially, there are no groups.

For Gromos96 force fields, rlist=rcoulomb=0.9 and rvdw=1.4 are correct settings. 
  I suspect you're trying to use some sort of switch or shift function, and 
hence rlist > rvdw.  You shouldn't.  vdwtype=cutoff and coulombtype=PME are the 
best settings.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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