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-- 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/ <https://sites.google.com/site/bakercompchemlab/> On Mon, Mar 2, 2015 at 8:38 PM, David A Case <case.biomaps.rutgers.edu> wrote: > 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. > > ....dac > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Mon Mar 02 2015 - 20:30:02 PST