Hi Marc, Ken, Lalith,
I have used the the following in preparing the prmtop and inpcrd file
source /usr/soft/amber12/dat/leap/cmd/leaprc.ff12SB
loadAmberparams /usr/soft/amber12/dat/leap/parm/frcmod.ionsjc_tip3p
Does AMBER12 have these have the new 12-6 and 12-6-4 parameters.
Best,
Bergy
On Tue, Dec 2, 2014 at 1:33 PM, Marc van der Kamp <marcvanderkamp.gmail.com>
wrote:
> Hi,
> Well, I would say it is best to do without restraints. It is likely you
> won't need them; if the ATP phosphate groups stay reasonably in place, then
> the electrostatic interactions between Mg2+ and the negative partial
> charges of the phosphate oxygens will keep them together.
> But it is important to monitor what happens in the simulation.
> Also, consider the Mg2+ parameters you want to use; you may want to
> consider the more recent Mg2+ VdW parameters from Allner et al. (see
> below).
>
> If you find the Mg2+ doesn't stay in place (even with the updated
> parameters), you could consider distance restraints, but this is certainly
> not ideal.
>
> Good luck,
> Marc
> Olof Allnér, Lennart Nilsson, and Alessandra Villa
> *J. Chem. Theory Comput.* *2012* 8:1493-1502
> *Magnesium Ion-Water Coordination and Exchange in Biomolecular Simulations*
>
> On 2 December 2014 at 19:59, BERGY <nucleic81.gmail.com> wrote:
>
> > Hi amber -users,
> >
> > I have a protein crystal structure with ATP in the ligand site and a
> > coordination bond with 6 oxygen atoms. i.e. three from water oygen, OH
> > from Serine, two oxygens from ATP. They all are within 2.1 Angstroms from
> > the Ion. The question is, while carrying out the simulation, Is it
> > necessary to have some distance or angle or dihedral restraints to
> maintain
> > the coordination bonds.
> >
> > Best,
> > Bergy
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Received on Tue Dec 02 2014 - 14:00:02 PST
