[gmx-users] Regarding error during genion step before energy minimization

Justin A. Lemkul jalemkul at vt.edu
Fri Mar 11 14:51:15 CET 2011

Meenakshi wrote:
> Hi,
> I am doing MD simulation of protein-ligand system using G53a6 as 
> forcefield. I got the ligand.itp file for ffG53a6 from the ATB 
> (Automated Topology Builder) server. I included the ligand.itp in the 
> .top file, generated an octahedron solvation box, solvated it and did 
> the grompp step before energy minimization. It was fine so far. However, 
> when I performed the genion step to neutralize the charge on the system, 
> it threw an error:
> -------------------------------------------------------
> Program genion, VERSION 4.0.5
> Source code file: ../../../../src/mdlib/ns.c, line: 2193
> Fatal error:
> Max #atoms in a charge group: 33 > 32
> -------------------------------------------------------
> My ligand has 33 atoms.
> While searching the mailing list for a solution to this problem I came 
> across this link
> http://comments.gmane.org/gmane.science.biology.gromacs.devel/2846
> I assume this is a bug in Gromacs 4.0.5. Has the bug been fixed?
> Please help me find a solution to this problem.

IIRC, there have been changes to the maximum allowable size to a charge group, 
but instead of thinking of this problem as a bug, you should really consider the 
fact that no sensible charge group should ever have that many atoms, let alone 
encompass an entire molecule!  You will have significant artifacts in nonbonded 
interaction calculations.  Garbage in, garbage out as the saying goes.


> Thanks,
> Meenakshi Pradhan
> TCS Innovations Lab
> Tata Consultancy Services Ltd
> Madhapur, Hyderabad
> India
> mail: meenakshi at atc.tcs.com


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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