AMBER Archive (2002)

Subject: Re: several questions

From: David A. Case (case_at_scripps.edu)
Date: Tue Jul 23 2002 - 19:08:10 CDT

On Tue, Jul 23, 2002, David Keller wrote:

> Is there a pre-defined residue type for FULL nucleotides, including
> the tri-phosphate?
> Is there a pre-defined triphospate defined as a residue in its own
> right?
> Is there some standard way to deal with this problem?

You'd think there should be, and I keep hoping that people that have worked
with di- and tri-phosphates would contribute to Richard Bryce's database
(see the "contributed parameters" link on the Amber Web page). Maybe someone
on the list will have parameters to share....

Antechamber should be able to handle this, but I haven't tried molecules like
this yet. You might try creating a pdb file and giving antechamber a try.

>
> 2. Our molecule also has magnesium ions bound to it. Is there a
> predefined set of parameters (or residue, or atom, or unit) for
> magnesium ions?

Divalent ions are tough. For outer-sphere complexes (where the 6 closest
waters are always bound to the ion, you could look at:

%A V. Tsui
%A D.A. Case
%T Calculations of the Absolute Free Energies of Binding between RNA and Metal
Ions Using Molecular Dynamics Simulations and Continuum Electrostatics
%J J. Phys. Chem. B
%V 105
%P 11314-11325
%D 2001

For a discussion of some of the issues involved:

%A T. Dudev
%A C. Lim
%T Incremental Binding Free Energies in Mg2+ Complexes: A DFT Study
%J J. Phys. Chem. A
%V 103
%P 8093-8100
%D 1999

>
> 3. After running the tutorial on polyAT we tried to animate it using
> VMD, but VMD would not read the prmtop and inpcrd files. It gave us a
> message "Not equipped to read perturbation parm file". Is this a known
> problem? Have formats changed recently?
> Thanks,

Formats *have* changed, and perhaps VMD thinks you have a perturbation file
(I'm assuming you don't...). You could use newparm2old to convert your
prmtop file to the earlier format, and see if VMD is any happier. But that's
just a guess -- I'm not a VMD user myself.

..good luck...dac 

-- 

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