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Solvation free energies of amino acid side chain analogs for common molecular mechanics water models
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10.1063/1.1877132
/content/aip/journal/jcp/122/13/10.1063/1.1877132
http://aip.metastore.ingenta.com/content/aip/journal/jcp/122/13/10.1063/1.1877132

Figures

Image of FIG. 1.
FIG. 1.

Differences in partial charges between (left) the OPLS-AA parameter set serine side chain and (right) the OPLS-AA-derived parameters used for the side chain analog in this study. Only the carbon changes in charge.

Tables

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Table I.

Correspondence between amino acids and the amino acid side chain analogs used in this study, and the naturally occurring frequency of the amino acids in proteins (Ref. 41).

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Table II.

Model input parameters and pure liquid properties for SPC, SPC∕E, TIP3P, TIP4P, TIP3P-MOD, and TIP4P-Ew water models. Uncertainties for the density are all , for the heat of vaporization are , for the free energies are , and for the self-diffusion constant are . Computation of the heat of vaporization, including the polarization correction, was done according to previously published methods (Ref. 29). Water experimental data of and come from Refs. 13 and 10, respectively.

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Table III.

Free energy of solvation of amino acid side chain analogs in published water models in Table II. Average deviations from experiment are presented in Table V. All results in . Uncertainties of the individual free energy solvation used in the average are , roughly proportional to molecular size. TIP4P, SPC∕E, and TIP4P-Ew have longer diffusion times, hence longer water decorrelation times, and hence slightly larger uncertainties within that range for each amino acid side chain analog.

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Table IV.

Free energy of solvation of amino acid side chain analogs in TIP3P, TIP3P-MOD, and the Lennard-Jones modified water parameters presented in Table VII. Average deviations from experiment are presented in Table VI. All result in . Uncertainties of the individual free energy solvation used in the average are , roughly proportional to molecular size.

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Table V.

Free energy of solvation of amino acid side chain analogs in published water models. The values for “Slope” and “Constant” are from the linear fit from the flat averages over the 15 side chain analogs. All averages and root mean square (rms) errors in . Uncertainties of the individual free energy solvation used in the average are .

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Table VI.

Free energy of solvation of amino acid side chain analogs in TIP3P, TIP3P-MOD, and the Lennard-Jones modified water parameters presented in Table VII. The values for slope and constant are from the linear fit from the flat averages over the 15 side chain analogs. All averages and root mean square (rms) errors in . Uncertainties of the individual free energy solvation used in the average are .

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Table VII.

, and pure liquid properties for TIP3P, TIP3P-MOD, and novel Lennard-Jones-modified waters M20-M25. All model parameters except for and are the same as TIP3P, as shown in Table II. Uncertainties in density are , for the heat of vaporization are , for the free energies are , and for the self-diffusion constants are . Computation of the heat of vaporization was done according to previously published methods (Ref. 29), but without the polarization correction.

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/content/aip/journal/jcp/122/13/10.1063/1.1877132
2005-04-07
2014-04-24
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Solvation free energies of amino acid side chain analogs for common molecular mechanics water models
http://aip.metastore.ingenta.com/content/aip/journal/jcp/122/13/10.1063/1.1877132
10.1063/1.1877132
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