Re: [AMBER] calculation of the binding energy in amber 12 or 14

From: Saikat Pal <>
Date: Wed, 24 May 2017 05:09:30 +0000 (UTC)

Dear Sir,  Thank you for your reply. I have read the 3D-RISM part in amber 14 manual and also seen in ../AMBER/amber14/dat/rism1d/model
path there is no Strontium model (.mdl file for Strontium ). What should I do ?? please help me.
Thanks and regards,Saikat Pal

    On Saturday, 20 May 2017 6:56 PM, David A Case <> wrote:

 On Fri, May 19, 2017, Saikat Pal wrote:

>  I want to calculate the binding energy using MMGBSA/MMPBSA of DNA and
>  Strontium ion (Sr+2).Is it possible in amber 14 or 12 ??

Can't really be done in any version of Amber.  We wrote a paper years ago
outlining the problems with estimating metal ion affinities via mmPBSA:

%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

Old, but I think the caveats are still valid: the answer depends so heavily
on the parameters one assigns to the ion as to be nearly meaningless.  In
my view, studies of divalent ions really need explicit waters (and are still
very difficult).  3D-RISM might be an alternative approach, but that is very
much an active research area.


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