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

[Justin Lemkul]

On 6/18/14, 6:47 AM, sucharita dey wrote:
> Thanks Justin. The OGA topology is now OK. But still the problem with the
> FE ion persists (very high force on it) during the minimization.
> Yes, I want to link the FE with its co-ordination atoms by simple harmonic
> (bond type 6), can you please tell what will be the value for kb (the force
> constant)?
>

No idea.  If there are no vibrational data available for the interaction, you're 
stuck with using some arbitrary value.  That's actually somewhat common when 
dealing with transition metals, because that's the least of your worries when it 
comes to such species; MM representations of such metals are very poor in general.

-Justin

>
> On Fri, Jun 13, 2014 at 8:41 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> 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 connections.
>>
>>   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
>>
>> --
>> ==================================================
>>
>> 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
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

==================================================