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

sucharita dey sucharita.dey at gmail.com
Fri Jun 13 08:11:05 CEST 2014

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.

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).

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.

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

Sorry for this long ugly query, shall be thankful for any help.


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