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

[sucharita dey]

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)?


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
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>