H.A.Carlson, K.L.Meagher, L.T.Redman
College of Pharmacy, University of Michigan, USA


Meagher KL, Redman LT, Carlson HA
Journal of Computational Chemistry 2003,24,1016
Development of polyphosphate parameters for use with the AMBER force field
Accurate force fields are essential for reproducing the conformational and dynamic behavior of condensed-phase systems. The popular AMBER force field has parameters for monophosphates, but they do not extend well to polyphorylated molecules such as ADP and ATP. This work presents parameters for the partial charges, atom types, bond angles, and torsions in simple polyphosphorylated compounds. The parameters are based on molecular orbital calculations of methyldiphosphate and methyltriphosphate at the RHF/6-31+G* level. The new parameters were fit to the entire potential energy surface (not just minima) with an RMSD of 0.62 kcal/mol. This is exceptional agreement and a significant improvement over. the current parameters that produce a potential surface with an RMSD of 7.8 kcal/mol to that of the ab initio calculations. Testing has shown that the parameters are transferable and capable of reproducing the gas-phase conformations of inorganic diphosphate and triphosphate. Also, the parameters are an improvement over existing parameters in the condensed phase,as shown by minimizations of ATP bound in several proteins. These parameters are intended for use with the existing AMBER 94/99force field, and they will permit users to apply AMBER to a wider variety of important enzymatic systems. 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1016-1025, 2003.


Guide to using polyphosphate parameters:

We have recently parameterized di- and tri- phosphate tails for use with the AMBER95 force field. The parameters are based on reproduction of RHF/6-31+G* potential surface. Methyldiphosphate and methyltriphosphate were used as model compounds. To most accurately model the behavior of the polyphosphates an additional atom type for the terminal anionic oxygens, O3, was added. The RESP methodology was used to assign partial charges.

ADP.prep, ATP.prep
- AMBER6 prep files for ADP and ATP. RESP partial charges are given in the last column.
- Atom names (ie: C4*, PB, O3G) must match the atom names as given in the pdb.

- Need to copy the leaprc file to your working directory and modify it to contain the O3 atom type.

{ "O" "O" "sp2" }
{ "O3" "O" "sp2" }
{ "O2" "O" "sp2" }
{ "OW" "O" "sp3" }

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Last modified Fri Jun 29 17:44:33 BST 2001