|
606. AMSOL: An SCF Program Incorporating Free Energies in
Aqueous Solution and Semiempirical Charge Models (Version
5.0)
by Christopher J. Cramer,a Gregory D. Hawkins,a
Gillian C. Lynch,a David J. Giesen,a Ivan Rossi,a Joey W.
Storer,a Donald G. Truhlar,a and Daniel A. Liotardb
aDepartment of Chemistry, University of Minnesota,
Minneapolis, MN 55455
bLaboratoire de Physicochemie Théorique, Universite
de Bordeaux, France
(based on ampac+version 2.1 by D. A. Liotard, E. F.
Healy, J. M. Ruiz, and M. J. S. Dewar and including options
from gepol by E. Silla, I. Tuñon, and J. L. Pascual-Ahuir
and from EF by Frank Jensen)
amsol is a semiempirical quantum chemistry program that
includes the MINDO/3, MNDO, AM1 and PM3 Hamiltonians, the
CM1A and CM1P class IV charge models for calculating partial
atomic charges, SM1+SM3.1 solvation models for calculating
free energies of solvation in water, and the SM4 solvation
model for calculating free energies of solvation in alkanes.
Geometry optimization is possible in both the gas phase and
solution.
Solvation effects are included via two terms. The
first accounts for electrostatic polarization of the solvent
by the generalized Born approximation based on a distributed
monopole representation of the solute charges with
dielectric screening. Solute polarization is also included
self-consistently. The second term is proportional to the
solvent-accessible surface area, with a set of
proportionality constants (surface tensions) which depend on
the local nature of the solute for each atom or group's
interface with the solvent. This version of amsol contains
the AM1-SM1, AM1-SM1a, AM1-SM2, AM1-SM2.1, PM3-SM3, and PM3-
SM3.1 parameter sets for water and the SM4 set for alkanes.
The latter may be used with either AM1 or PM3. Parameters
are available for H, C, N, O, F, P, S, Cl, Br, and I in all
aqueous solvation models and for all these atom types except
P in the alkane models.
Upon request amsol can calculate Charge Model 1 (CM1)
partial charges during gas-phase calculations and SM4
solution phase calculations. CM1 charges are a
semiempirical mapping of the NDDO Mulliken population
analysis charges such that the CM1 charges more accurately
reproduce experimental gas-phase dipole moments and high
level ab initio partial charges. This version of amsol
contains the CM1A and CM1P models, which are specific to the
AM1 and PM3 Hamiltonians, respectively
The main enhancement in version 5.0 is the inclusion of
the AM1-SM4 and PM3-SM4 solvation models for alkanes. These
models use class IV charges and can calculate the free
energy of solvation for any alkane [including, e.g., n-
hexadecane for pharmaceutical modeling, n-hexane,
cyclohexane, and iso-octane (2,2,4-trimethylpentane)] . The
mean unsigned error for these models is 0.34 kcal/mol for
AM1-SM4 and 0.33 kcal/mol for PM3-SM4, as measured against
506 solute/solvent pairs used in the parameterization.
Two other enhancements in amsol+version 5.0 are related
to geometry optimization. First of all, amsol incorporates
the eigenvector following (EF) algorithm, based on code
written originally by Frank Jensen. EF is an efficient
optimizer with many useful options, and it is especially
well suited for finding saddle points. Second, we have
introduced a new keyword, called KICK, that greatly reduces
the number of calculations terminating with the familiar
message "line minimization failed twice in a row."
Who should upgrade to version 5.0 for solvation-phase
calculations?
ä Persons using versions earlier than 3.5 who wish
to take advantage of the increased speed of versions 3.5 and
later. Versions 3.5 and 4.0 are respectively factors of
about 3 and 20 faster than version 3.0.1 for aqueous phase
calculations at the same precision on Unix workstations.
ä Persons having versions earlier than 4.1 who make
frequent use of the AM1-SM2 aqueous-phase model for large
molecules because the AM1-SM2.1 model in versions 4.1 and
later provides similar quality results but allows for
faster, variable-precision calculations for exploratory
work.
ä Persons having versions of amsol prior to 4.6
* who make frequent use of the PM3-SM3 aqueous-
phase model because the PM3-SM3.1 model in version 4.6 and
later provides similar quality results but allows for
faster, variable-precision calculations for exploratory work
* who wish to use the improved "restart"
options
* who wish to use the MULLIK keyword (Mulliken
analysis in a de-orthogonalized basis)
ä Persons having versions of amsol prior to 5.0
* who wish to calculate solvation free energies
or class IV partial charges in alkanes using the new AM1-SM4
and PM3-SM4 models
* who wish to take advantage of the improved
convergence properties of the EF algorithm for transition
states
* who wish to use the new KICK keyword in
version 5.0 that eliminates most error terminations
associated with failure of line minimizations
In addition to these features for solution-phase
calculations we note that amsol can also perform gas-phase
calculations, that it is a very portable code in Unix
environments, and that it has an extensive test suite. In
addition, versions 4.5 and later include class IV partial
charges for isolated (i.e., gas-phase) molecules. The class
IV partial charges in versions 4.5 and later are more
accurate than HF/6-31G* electrostatic fitting (ChelpG or
other methods) charges, but the cost is essentially
identical to AM1 or PM3 Mulliken charges, i.e., very much
smaller than the cost of HF/6-31G*-ChelpG charges. For
these reasons, amsol may be the semiempirical package of
choice even for some applications that do not take advantage
of its solution-phase capabilities.
The solvation and charge models are described further
in the following references:
AM1-SM1 and AM1-SM1a: "General Parameterized SCF Model
for Free Energies of Solvation in Aqueous Solution," C. J.
Cramer and D. G. Truhlar, Journal of the American Chemical
Society 113, 8305-8311, 9901(E) (1991).
AM1-SM2: "An SCF Solvation Model for the Hydrophobic
Effect and Absolute Free Energies of Aqueous Solvation," C.
J. Cramer and D. G. Truhlar, Science 256, 213-217 (1992).
PM3-SM3: "PM3-SM3: A General Parameterization for
Including Aqueous Solvation Effects in the PM3 Molecular
Orbital Model," C. J. Cramer and D. G. Truhlar, Journal of
Computational Chemistry 13, 1089+1097 (1992).
overview: "AM1-SM2 and PM3-SM3 Parameterized SCF
Solvation Models for Free Energies in Aqueous Solution," C.
J. Cramer and D. G. Truhlar, Journal of Computer-Aided
Molecular Design 6, 629+666 (1992).
ASA algorithm and other computational improvements
introduced in versions 4.0 and 4.1: "Improved Methods for
Semiempirical Solvation Models," D. A. Liotard, G. D.
Hawkins, G. C. Lynch, C. J. Cramer, and D. G. Truhlar,
Journal of Computational Chemistry, in press. Preprints are
available from Research Reports Coordinator, Supercomputer
Institute, 1200 Washington Avenue South, Minneapolis, MN
55415; request UMSI preprint number 94/143.
CM1A and CM1P: "Class IV Charge Models: A New
Semiempirical Approach in Quantum Chemistry," J. W. Storer,
D. J. Giesen, C. J. Cramer, and D. G. Truhlar, Journal of
Computer-Aided Molecular Design, in press. Preprints are
available from Research Reports Coordinator, address above;
request UMSI preprint number 94/144.
first paper on SM4 alkane models: "A General
Semiempirical Quantum Mechanical Solvation Model for
Nonpolar Solvation Energies. n-Hexadecane," D. J. Giesen, J.
W. Storer, C. J. Cramer, and D. G. Truhlar, Journal of the
American Chemical Society 117, 1057+1068 (1995).
amsol-version 5.0 has been tested on Cray C90, Cray-2,
DEC 3000/500X AXP, IBM RS/6000, IRIS Indigo R4000, and Sun
SPARCStation computers running the Unix operating system.
The code is distributed as a tar file containing 205 files,
including FORTRAN source code and C shell scripts for
compiling and linking, for interactive job submission, and
for submitting batch jobs under the NQS queuing system. The
distribution also includes a brief on-line manual (ASCII
documentation file), a Postscript version of an
ampac+version 2.1 documentation file, and a 75-run test
suite.
_______
FORTRAN 77 with INCLUDE extension
Lines of FORTRAN code: 37,992
Total length of distribution files, including FORTRAN
code, optional C timing utility, Unix scripts, test suite,
and documentation files: 80,711 lines
|
