Automatic force field
parameter assignment in YASARA
YASARA provides an advanced approach to simulate 98% of the PDB at the
touch of a button (manual intervention is needed for proteins with a
Calpha only backbone or very exotic metal ions). AutoSMILES employs
SMILES strings to identify known molecules (even if residue and atom
names differ) and resorts to the AM1BCC and GAFF
(General AMBER force field) approaches for all other molecules. AM1BCC
are additionally improved by using known RESP charges of similar
molecule fragments, again identified via SMILES strings.
The individual AutoSMILES steps can be summarized as follows:
- Assignment of pH dependent
fractional bond orders and protonation patterns, typing of ring systems by a graph-theoretic approach.
- Identification of known molecules (from the force field
definition file, the AMBER
Parameter Database or GLYCAM) using SMILES strings. If no hit is found,
proceed to step 3.
- Calculation of semi-empirical AM1 Mulliken point
This step involves a geometry optimization with the COSMO solvation
model and avoids fatal rearrangements sometimes found when
highly charged molecules like ATP(4-) in
- Assignment of AM1BCC atom- and bond types.
- Application of the 'AM1 Bond Charge Correction' to
improve the AM1 charges and make them better represent the
electrostatic potential around the molecule - just like RESP charges.
- Further improvement of the AM1BCC charges using the
ideal RESP charges of similar molecule fragments, identified via SMILES
- Assignment of GAFF (General AMBER Force Field) atom
and remaining force field parameters.
- In the end, the newly created parameters are cached
instantaneous availability next time.
Since all this is done automatically, only one
step is required in
practice: Press <F12> to run the simulation. YASARA also produces
a detailed force field parameter assignment report, including PREP
topologies and FRCMOD files for all newly parameterized molecules, that
can be plugged directly into other MD programs like AMBER.
an integral part of YASARA Dynamics
and can additionally be tested via a web server.
R E F E R E N C E S
 Fast, efficient generation of
high-quality atomic charges. AM1-BCC model: II. Parameterization and
Jakalian A, Jack DB and Bayly CI (2002) J Comput Chem 23,1623-1641
 Development and Testing of a General Amber Force Field
Wang J, Wolf RM, Caldwell JW, Kollman PA and Case DA (2004) J Comput
Chem 25, 1157-1174.
 MOPAC: A semiempirical molecular orbital program
Stewart JJP (2000) J.Comp.Aided Mol.Des. 4,1-103
 Conductor-like screening model for real solvents: a new
approach to the quantitative calculation of solvation phenomena
Klamt A (1995) J.Phys.Chem. 99, 2224-2235