Bouke P.
van Eijck, Department of Crystal and Structural
Chemistry, Bijvoet Center for Biomolecular
Research, Utrecht University, Padualaan 8, 3584 CH
Utrecht, The Netherlands. E-mail: vaneyck@chem.uu.nl
or vaneijck@xs4all.nl.
For
information on the standard UPACK package, see the main
manual .
As
discussed in the main manual, the force field is defined by the file upack/tops/ffname.ff. As an example for the Buckingham potential, the
Williams and Starr [1] force field for benzene can be found
in benz.ff. Here we shall discuss Lennard-Jones type
force fields for carbohydrates in some detail. For the first stage (program pack12) we used the force
field UNITAT, which was developed from GROMOS87 [2] by
optimizing geometric crystal data for 23 carbohydrate molecules [3].
In the final stage it is better to use an all-atom force field. In this way the
computations take less time; but note that some additional all-atom structures
may be found if that force field is used right from the beginning.
United-atom force fields for monosaccharides and polyalcohols
Atom types:
|
HO |
hydroxyl H |
|
OA |
hydroxyl O |
|
OS |
ether O
in ring and exocyclic OCH3 group |
|
CS0 |
C atom
without H in sugar ring |
|
CS1 |
united
CH1 group in sugar ring |
|
CS2 |
united CH2
group in sugar ring and exocyclic CH2OH group |
|
CH3 |
united CH3 group |
Entries in the force field files
refer to the Lennard-Jones potential; energy units
are kcal/mol, distance units Angstrom. Every C-C bond
separates two of the following charge groups:
|
CH3 |
0.00 |
|
CS2 |
0.00 |
|
C-O-H |
0.15, -0.50, 0.35 |
|
C-O-C |
0.18, -0.36, 0.18 |
|
C-O-C-O-H |
0.20, -0.36, 0.31, -0.50, 0.35 |
|
C-O-C-O-CH3 |
0.15, -0.36, 0.17, -0.36, 0.17 |
|
C-O-C-O-CS2 |
0.16, -0.36, 0.17, -0.36, 0.16 |
|
C-O-C-O-C-O-C |
0.14, -0.36, 0.40, -0.36, 0.40, -0.36, 0.14 |
All-atom force fields for monosaccharides and polyalcohols
Many force
fields depend on atomic charges from ab-initio quantumchemical
calculations. For carbohydrates, with their high conformational flexibility, this
is rather unpractical. Carbohydrate force fields with fixed standard charges
have been proposed by Ha et al [4], Kouwijzer et al [5] and Damm et al [6]. We have compared
the rankings of the experimental structures in a test set of 15 molecules for
these force fields [7], and found that the third force field
(OPLS) gives the best results. Nevertheless, it is not superior to UNITAT and
we have not been able to develop an all-atom force field that performs better.
Polarization, although theoretically necessary to account for the cooperativity of hydrogen bonds, gave no improvement at
all.
The OPLS
parameters can be found in file opls.ff, the two other force
fields in the files ha.ff and milou.ff. All these force fields
use the Lennard-Jones potential; in the OPLS force
field all 1...4 interactions are scaled by 0.5. A cutoff of at least 10 A or,
preferably, Ewald summation should be used. No improper dihedrals are
necessary.
Atom types:
|
HO |
hydroxyl H |
|
HC |
aliphatic H |
|
OA |
hydroxyl oxygen |
|
OS |
ether oxygen in ring |
|
OE |
hydroxyl
oxygen in exocyclic CH2OH group |
|
CA |
anomeric carbon atom |
|
CS |
other ring carbon atoms |
|
CE |
exocyclic carbon atom |
The charges in the OPLS force field
are found by the following rule: each bond carries a "bond increment"
which contributes equal positive and negative charges to the two atoms
involved.
|
Negative side |
Positive side |
Bond increment |
|
|
OA (anomeric) |
HO |
0.435 |
|
|
OA (other) |
HO |
0.418 |
|
|
OA |
C |
0.265 |
|
|
OS, OE |
C |
0.200 |
|
|
C |
C |
0 (dividing charge groups) |
|
|
CA |
HC |
0.10 |
|
|
C (with OH group) |
HC |
0.06 |
|
|
C (other) |
HC |
0.03 |
All-atom force fields for carboxylic acids
As
discussed in Ref. [8], we have made a few changes and
extensions in the OPLS force field for the modelling of carboxylic acids (the
"OPLS-AC" force field). This extension is only a first try, and is by
no means fully optimized. The parameters are included in the file opls.ff; charges are as published in Ref. [8].
Atom types:
|
C |
C in COOH |
|
O |
=O in COOH |
|
OZ |
-O in COOH |
|
HZ |
H in COOH |
|
CS |
aliphatic C |
|
HC |
H on C or CS |
|
OA |
hydroxyl O |
|
HO |
hydroxyl H |
All-atom force fields for aromatic systems
Due to
conjugation, each aromatic system is unique in principle: geometry parameters
and charges have to be derived from theoretical chemistry. For simple chloro- and bromo substituted
benzenes a few standard parameters are available in UPACK [9].
For structure generation Lennard-Jones parameters can
be taken from the file opls.ff. Buckingham parameters,
mostly taken from the publications of Williams and Price, are available in the
file will.ff. In both files intramolecular parameters were taken rather arbitrarily.
Atom types:
|
CR61 |
united-atom
benzene CH group |
|
CR |
united-atom
central C atom or all-atom aromatic C |
|
HR |
aromatic H |
|
Cl |
chlorine |
|
Br |
bromine |
Every C-C bond separates two charge
groups:
|
CR61 |
0.00 |
|
CR-HR |
-0.10, +0.10 (+/- 0.15 in will.ff) |
|
CR-Cl |
+0.10, -0.10 |
|
CR-Br |
+0.10, -0.10 |
1. D. E. Williams and T. L. Starr, Comput. Chem. 1 (1977) 173-177.
2. W. F. van Gunsteren and H. J. C. Berendsen,
GROMOS, Groningen molecular simulation
package, University of Groningen, 1987.
3. B. P. van Eijck and J. Kroon, J. Comput. Chem.
20 (1999) 799-812.
4. S. N. Ha, A. Giammona, M. Field and J. W. Brady, Carboh. Res. 180 (1988)
207-221.
5. M. L. C. E. Kouwijzer, B. P. van Eijck, S. J.
Kroes and J. Kroon, J. Comput.
Chem. 14 (1993) 1281-1289.
6. W. Damm, A. Frontera, J.
Tirado-Rives and W. L. Jorgensen, J. Comput. Chem. 16 (1997) 1955-1970.
7. B. P. van Eijck and J.
Kroon, J. Comput. Chem. 20
(1999) 799-812.
8. B. P. van Eijck, J. Comput.
Chem. 23 (2002) 456-462.
9. B. P. van Eijck, Phys. Chem. Chem. Phys.
4 (2002) 4789-4794.