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.
-Justin
Thanks,
Meenakshi Pradhan
TCS Innovations Lab
Tata Consultancy Services Ltd
Madhapur, Hyderabad
India
mail: meenak...@atc.tcs.com
--
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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