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Calculation of the water–cyclohexane transfer free energies of neutral amino acid side‐chain analogs using the OPLS all‐atom force field
Author(s) -
MacCallum Justin L.,
Tieleman D. Peter
Publication year - 2003
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.10328
Subject(s) - solvation , chemistry , cyclohexane , thermodynamic integration , histidine , molecular dynamics , side chain , force field (fiction) , opls , glycine , atom (system on chip) , computational chemistry , amino acid , water model , molecule , organic chemistry , biochemistry , physics , quantum mechanics , polymer , computer science , embedded system
We calculated the free energy of solvation of the neutral analogs of 18 amino acid side‐chains (not including glycine and proline) using the OPLS all‐atom force field in TIP4P water, SPC water, and cyclohexane by molecular dynamics simulation and thermodynamic integration. The average unsigned errors in the free energies of solvation in TIP4P, SPC, and cyclohexane are 4.4, 4.9, and 2.1 kJ/mol respectively. Most of the calculated hydration free energies are not favorable enough compared to experiment. The largest errors are found for tryptophan, histidine, glutamic acid, and glutamine. The average unsigned errors in the free energy of transfer from TIP4P to cyclohexane and from SPC to cyclohexane are 4.0 and 4.1 kJ/mol, respectively. The largest errors, of more than 7.5 kJ/mol, are found for histidine, glutamine, and glutamatic acid. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1930–1935, 2003