[gmx-users] Problem in energy minimization and further dynamics probably for atomic clashes

Justin Lemkul jalemkul at vt.edu
Fri Jun 13 14:43:22 CEST 2014

On 6/13/14, 2:11 AM, sucharita dey wrote:
> Dear Users,
> I have a protein-DNA system with 3 Zinc fingers, 1 Fe++, 1 cofactor NOG
> (N-OxalyGlycine) and crystal waters.
> I have generated the initial topology of OGA from PRODRG and incorporated
> it in the  the forcefield gromos 53a6 and since the forcefield already has
> parametrs for ZN and FE, I had no problem in generating the  *.itp files. I
> solvated the system and ran steep minimization for 1000 steps with emstep =
> 0.1 and emtol 1.

Is the NOG topology sound?  PRODRG has known problems getting charges right, but 
building a suitable NOG topology from existing building blocks is trivial.

> It ran for ~80 steps and stopped. I checked the gro file generated, the
> problem is around OGA and the FE,  and the OGA is loosing its structure. I
> suspect it due to clashes, -- actually in the crystal structure 2 oxygens
> of OGA are in co-ordination with the FE (the FE being co-ordinated with 4
> other atoms including one O from crystal water).

Sounds like a potential topology issue.  One simple test is to run NOG in vacuo 
then in a box of water to see if it is stable on its own, then deal with it in 
the context of the full protein+ions.

> I have not considered the FE co-ordination, can you please suggest how to
> do this or else please suggest if you feel the problem is elsewhere.

Ion coordination is easily done with distance restraints or type-6 harmonic 

> Below is the comment given after minimization stopped:
> *Energy minimization has stopped, but the forces havenot converged to
> therequested precision Fmax < 1 (whichmay not be possible for your system).
> Itstoppedbecause the algorithm tried to make a new step whose sizewas
> toosmall, or there was no change in the energy sincelast step. Either way,
> weregard the minimization asconverged to within the available
> machineprecision,given your starting configuration and EM parameters.Double
> precision normally gives you higher accuracy, butthis is often notneeded
> for preparing to run moleculardynamics.writing lowest energy
> coordinates.Steepest Descents converged to machine precision in 84
> steps,but did not reach the requested Fmax < 1.Potential Energy  =
> -3.7139549e+08Maximum force     =  7.7602650e+14 on atom 4207Norm of
> force     =  3.6179670e+12*
> NOTE: the atom 4207 with maximum force is FE

You have essentially infinite forces, which indicate very bad geometry, clashes, 
or a bad topology.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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