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