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Volumn 119, Issue 11, 2003, Pages 5740-5761

Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; COMPUTER SIMULATION; FREE ENERGY; HYDRATION; MOLECULAR DYNAMICS; STATISTICAL METHODS;

EID: 0141990949     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.1587119     Document Type: Article
Times cited : (593)

References (107)
  • 5
    • 0011373830 scopus 로고
    • edited by V. Renugopalakrishnan, P. R. Carey, I. C. P. Smith, S. G. Huang, and A. C. Storer (ESCOM, Leiden)
    • H. J. C. Berendsen, in Proteins: Structure, Dynamics, and Design, edited by V. Renugopalakrishnan, P. R. Carey, I. C. P. Smith, S. G. Huang, and A. C. Storer (ESCOM, Leiden, 1991), pp. 384-392.
    • (1991) Proteins: Structure, Dynamics, and Design , pp. 384-392
    • Berendsen, H.J.C.1
  • 24
    • 0141875295 scopus 로고    scopus 로고
    • In this paper, the force fields are listed alphabetically
    • In this paper, the force fields are listed alphabetically.
  • 29
    • 0141979142 scopus 로고    scopus 로고
    • note
    • Additionally, the time scales important for equilibration and sampling can be longer than for water. For example, our initial experiments with blocked amino acids in a 1-octanol/water mixture suggested correlation times for some degrees of freedom of at least 100s of picoseconds,
  • 39
    • 0141944405 scopus 로고    scopus 로고
    • Produced and distributed by the Professor Jay Ponder's research group at Washington University. Documentation and programs for TINKER
    • Produced and distributed by the Professor Jay Ponder's research group at Washington University. Documentation and programs for TINKER are available at http://dasher.wustl.edu/tinker/.
  • 41
    • 0141910041 scopus 로고    scopus 로고
    • note
    • 90 000 is the number of processors running Folding@Home worldwide at the time the paper was written. At the time the simulations were run, the number was closer to 30 000.
  • 46
    • 0141979141 scopus 로고    scopus 로고
    • edited by R. P. Grant (Horizon Scientific, Wymondham, Norfolk, U.K.) (in press)
    • S. M. Larson, C. D. Snow, M. R. Shirts, and V. S. Pande, in Computational Genomics, edited by R. P. Grant (Horizon Scientific, Wymondham, Norfolk, U.K., 2002) (in press).
    • (2002) Computational Genomics
    • Larson, S.M.1    Snow, C.D.2    Shirts, M.R.3    Pande, V.S.4
  • 54
    • 0141979140 scopus 로고    scopus 로고
    • EPAPS Document No. E-JCPSA6-119-521329 for parameter files and a brief description. A direct link to this document may be found in the online article's HTML reference section. The document may also be reached via the EPAPS homepage or from ftp.aip.org in the directory /epaps/. See the EPAPS homepage for more information
    • See EPAPS Document No. E-JCPSA6-119-521329 for parameter files and a brief description. A direct link to this document may be found in the online article's HTML reference section. The document may also be reached via the EPAPS homepage (http://www.aip.org/pubservs/epaps.html) or from ftp.aip.org in the directory /epaps/. See the EPAPS homepage for more information.
  • 63
    • 0141910039 scopus 로고    scopus 로고
    • note
    • To reduce the effect of the noise that occurs when the correlation function approaches 0, the tail of the function was replaced by a linear fit (for the purposes of integration) between the first time the normalized correlation function reaches 0.1 and the first time it reaches 0.0 by connecting these time points. Inspection indicated that a linear approximation is more accurate than an exponential fit. This process is simplistic (and fails if the correlation function is too far from monotonically decreasing in the tail), but is of sufficient accuracy here, since we ultimately require only one significant digit in the determination of uncertainty.
  • 65
    • 0141910040 scopus 로고    scopus 로고
    • note
    • In some simulations, the electrostatic potential is shifted before the switch is applied in order to minimize forces arising from sharply tapered potentials (Ref. 64). However, since all groups are neutral in these simulations, a shift actually has no net effect on intergroup interactions.
  • 68
    • 0141979139 scopus 로고    scopus 로고
    • note
    • An important but rarely commented upon artifact of periodic boundary conditions in that there is a system size dependence for any observable that has nonisotropic components (Refs. 103-105). The density of water depends on the nonisotropic dipole-dipole interaction between water molecules, especially in conjunction with finite-range treatments of electrostatic interactions. A recent study of TIP5P water (Ref. 75), as well as our unpublished results have found this size-dependence of density with finite-ranged Coulombic potentials, but more work is necessary to understand this phenomenon.
  • 74
    • 0141944404 scopus 로고    scopus 로고
    • See Ref. 54
    • See Ref. 54.
  • 87
    • 0141944403 scopus 로고    scopus 로고
    • note
    • OPLS-AA and AMBER used some free energy simulations to gauge the general applicability of the force field for free energy calculations, but force fields were not explicitly tuned to give correct free energies - nor could they, with the precision available at the time.
  • 88
    • 0141875294 scopus 로고    scopus 로고
    • note
    • l), which can be approximated by neglecting the volume in liquid state and assuming ideality the gas (Ref. 19) with an error of less than 0.01 kcal/mol.
  • 100
    • 0141875293 scopus 로고    scopus 로고
    • note
    • solv is referred to as W(s|l) in the work of Ben-Nairn and Marcus (Ref. 19). They refer to this as the coupling work, or the Gibbs free energy of interaction of s with the rest of the solution.
  • 101
    • 0141875292 scopus 로고    scopus 로고
    • note
    • s, since this choice gives the purely extensive expression for the Gibbs free energy of an ideal gas in Eq. (15). However, other choices give identical results for chemical potentials and solvation free energies.
  • 102
    • 0141979138 scopus 로고    scopus 로고
    • note
    • 0. We note first that the contribution to the internal pressure from the relative kinetic energy and the intramolecular contributions to the virial from the special molecule have a time average of 0 at all values of λ, and thus need not be considered. Second, we also couple the contributions to the internal pressure from the intermolecular interactions between the special molecule and the rest of the material simply by virtue of the fact that those energy and force components and consequently also their contribution to the virial are coupled. The difference between their treatment and ours is in the handling of the contribution to the internal pressure from the center-of-mass kinetic energy of the special molecule. However, since the effect of coupling this contribution corresponds to the second step in our four-step process, its contribution to the free energy of solvation will be zero. Thus, the contribution to the internal pressure from the molecular internal energy of the coupled molecule does not actually need to be included.


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