Contributors
H.A.Carlson, K.L.Meagher, L.T.Redman
College of Pharmacy, University of Michigan, USA
Reference
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.
Comments
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.
frcmod.phosphate
- 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