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

Meenakshi meenakshi at atc.tcs.com
Fri Mar 11 13:37:47 CET 2011

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

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.

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

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