Hydrogen atom of hydroxyl group does not have vdWs parameters if you use
GAFF. Maybe you can try GAFF2.
Dading Huang
On Mon, Nov 21, 2016 at 11:22 AM, David Cerutti <dscerutti.gmail.com> wrote:
> This sounds like the old problem that CHARMM had with 1:4 electrostatics
> defeating angle terms and allowing a proton with no Lennard-Jones
> parameters to collapse into an oxygen. If you can attach your topology and
> coordinates this would be helpful, but before you do that try running your
> minimization printing the energy at each step (ntpr = 1). If the
> electrostatics are shooting through the roof that would corroborate my
> guess. There are a number of solutions I could think of, but I'd have to
> know more about the system first. If the problem is what I have guessed,
> then you will need new parameters for the system at some level, but again
> I'd have to know more about what is there.
>
> If this is simply a problem related to the hydrogen:oxygen bond stretching
> to permit the collapse, then you're probably OK if you just set the bond
> stiffness to be very high during energy minimization and then run dynamics
> with SHAKE. If the bonded parameters are all normal looking and this still
> happens, though (which is pretty conceivable to me, as the phosphate is
> going to have large charges on the oxygens as well as the hydroxyl protons
> which will create a very strong electrostatic attraction), then you will
> need some more rigorous parameter development.
>
> Dave
>
>
> On Sun, Nov 20, 2016 at 9:45 PM, jinfeng liu <jinfengliu1119.gmail.com>
> wrote:
>
> > Dear Amber developers,
> >
> > Recently I am doing molecular dynamics simulation for a molecule
> > which contains a fully protonated phosphate group. The Antechamber is
> used
> > to generate the parameters for the molecule.The atomic charges are fitted
> > using RESP method in HF/6-31G* level. However, when I used these
> parameters
> > to minimize the molecule, the hydroxylic hydrogen atom always had a bad
> > contact with its neighboring oxygen atom which double bonded to the
> > phosphorus atom. And this lead to the failure of MD simulation. I tried
> the
> > BCC charges, but this problem was still existed. The initial structure of
> > the molecule is 100% OK. So, can anyone tell me how to solve this
> problem ?
> > Thanks in advance.
> >
> > Best,
> > Jinfeng
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Received on Sun Nov 20 2016 - 23:00:03 PST
