SYBYL force field

Tripos is a force field created at Tripos Inc. for inclusion in the Alchemy and SYBYL programs. It is sometimes called the SYBYL force field. Tripos is... 

SYBYL Force Field, Ver. 6.1, Tripos Associates, Inc., 1699 S Hanley Road, Suite 303, St. Louis, MO. 

Molecular mechanics simulations use the laws of classical physics to predict the structures and properties of molecules. Molecular mechanics methods are available in many computer programs, including MM3, HyperChem, Quanta, Sybyl, and Alchemy. There are many different molecular mechanics methods. Each one is characterized by its particular/orce eW. A force field has these components ... 

Theoretical models include those based on classical (Newtonian) mechanical methods—force field methods known as molecular mechanical methods. These include MM2, MM3, Amber, Sybyl, UFF, and others described in the following paragraphs. These methods are based on Hook s law describing the parabolic potential for the stretching of a chemical bond, van der Waal s interactions, electrostatics, and other forces described more fully below. The combination assembled into the force field is parameterized based on fitting to experimental data. One can treat 1500-2500 atom systems by molecular mechanical methods. Only this method is treated in detail in this text. Other theoretical models are based on quantum mechanical methods. These include ... 

The second dataset consists of 50 V-acetyl peptide amides (Table 2) these peptides have un-ionizable side chains and have previously been studied by Buchwald and Bodor (28). The three-dimensional structures of the di-peptides were built using the force field and partial charges of Kollman (29) as implemented in Sybyl 6.5.3. The initial random starting conformations were energy minimized in vacuo. For all calculations described herein, the dielectric of the medium was set to unity and the electrostatic cut-off distance was set to 16 A. For each molecule, the Sybyl Genetic Algorithm-based conformational search,... 

This chapter describes the basis of molecular mechanics models and introduces the SYBYL and MMFF force fields. It also compares and contrasts molecular mechanics and quantum chemical models. 

Molecular mechanics models differ both in the number and specific nature of the terms which they incorporate, as well as in the details of their parameterization. Taken together, functional form and parameterization, constitute what is termed a force field. Very simple force fields such as SYBYL, developed by Tripos, Inc., may easily be extended to diverse systems but would not be expected to yield quantitatively accurate results. On the other hand, a more complex force field such as MMFF94 (or more simply MMFF), developed at Merck Pharmaceuticals, while limited in scope to common organic systems and biopolymers, is better able to provide quantitative accounts of molecular geometry and conformation. Both SYBYL and MMFF are incorporated into Spartan. 

SYBYL. A Molecular Mechanics Force Field developed by Tripos, Inc. 

Typical force fields such as the Tripos force field available in Sybyl or CVFF 24 available in Biosym contain torsional terms tliat have the form ... 

The 3-D artemisinin analogue database was created with Sybyl 6.2 (Tripos Assoc., St. Louis, MO)154 using the reported crystal structure for artemisinin as a template. The structures were minimized using the Tripos force field in Sybyl 6.2, producing structures close to that of artemisinin. To best describe the aromatic side chains of some analogues, as well as the aliphatic nature of the artemisinin backbone, Gasteiger-Htickel charges were calculated for each of the compounds. 

From a procedural standpoint, the start and stop residues of each of the seven helices was first identified by hydropathy analysis by using Kyte-Doolittle19 hydropathy indices. Each of the seven helices was then built individually, essential hydrogens were added, and the peptides were minimized with the Kollman United Atoms force field within the Sybyl software suite (Tripos Associates, Inc.). Typically, steepest descent was used initially as the minimization method (25-50... 

By design, no conformational engine was implemented in DISCO, based on the assumption that at the time, no universal force fields and methods suitable for all types of compounds were available [53]. However, the commercial distributor Tripos provides access to 3D converters and conformational search engines such as Concord and Confort via the Sybyl interface. These algorithms will not be reviewed here as strictly seen they are not part of any pharmacophore identification program. The distance geometry approach has been used... 

Do not add hydrogen atoms yet. SYBYL works with a force field. In a force field, atom characteristics and intramolecular connections are defined by atom types. 

The MOLBD3 force field is available in the POLYMER module of the SYBYL simulation software of the Tripos Co., St. Louis MO. 

Molecular modeling with an AMBER-like and MM2 force fields. Batch conformational searching with BAKMDL. Interfaces to AMPAC, MacroModel, GAUSSIAN86, SYBYL, PCMODEL, CHEM-3D. VAX. 

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