Re: [AMBER] ATP and ADP-Pi simulations

From: David A Case <>
Date: Mon, 2 Mar 2015 20:38:22 -0500

On Mon, Mar 02, 2015, Joseph Baker wrote:
> I see that the Carlson group has some ADP and ATP parameters that have been
> developed for use with ff99SB. However, from my understanding, ff12SB or
> ff14SB are now recommended for protein simulation due to some improvements
> in how they treat protein secondary structure. Is anybody aware of whether
> the Carlson ADP/ATP parameters have been vetted against ff12SB or ff14SB,
> or if one should expect the modifications that went into those force-fields
> to break anything badly if they are used with the Carlson ADP/ATP
> parameters? I'm curious because I saw a recent (2013) nice paper from the
> Hummer group on F1-ATPase where they still used the combination of ff99SB
> with these Carlson parameters.

The ff12SB and ff14SB force fields retain the charges and Lennard-Jones
parameters from ff99SB, and just modify some of the torsions for proteins.

When you read/say that ADP/ATP parameters are developed "for use with
ff99SB", that means that its charges and non-bonded parameters were
developed in ways analogous to those of ff99SB. To the same extent, then,
such parameters are appropriate for use with ff12SB or ff14SB.

> Also, does anyone know if there are any parameters for HPO42- or H2PO4-
> floating around out there that have been tested with Carlson ADP +
> ff99SB/ff12SB/ff14SB? If not then I'll go with the antechamber + RED server
> route.

You might want to look at this:

%A T. Steinbrecher
%A J. Latzer
%A D.A. Case
%T Revised AMBER Parameters for Bioorganic Phosphates
%J J. Chem. Theory Comput.
%V 8
%P 4405-4412
%D 2012

Be aware, however, that most claims of "compatibility" are based on
similarities in the approach by which parameters were developed, and
(generally) much less on specific tests that distinguish between compatible
and non-compatible combinations.


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Received on Mon Mar 02 2015 - 18:00:04 PST
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