Hi,
What parameter set are you using? AMBER has newer 12-6 and 12-6-4 parameters that might work for you better. They can be found in these papers:
http://dx.doi.org/10.1021/ct400146w <
http://dx.doi.org/10.1021/ct400146w>
http://dx.doi.org/10.1021/ct400751u <
http://dx.doi.org/10.1021/ct400751u>
Good luck!
Kennie
> On Dec 2, 2014, at 2:59 PM, 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 - 13:00:02 PST
