[AMBER] ATP and ADP-Pi simulations

From: Joseph Baker <bakerj.tcnj.edu>
Date: Mon, 2 Mar 2015 16:04:45 -0500

Hi all,

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.

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


Joseph Baker, PhD
Assistant Professor
Department of Chemistry
C101 Science Complex
The College of New Jersey
Ewing, NJ 08628
Phone: (609) 771-3173
Web: http://bakerj.pages.tcnj.edu/
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Received on Mon Mar 02 2015 - 13:30:02 PST
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