Macs in Chemistry

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SZYBKI has been updated

 

OpenEye have just released an update to SZYBKI with a host of new features. SZYBKI is used to optimise the three dimensional structure of molecules prior to their use in other programs. SZYBKI also refines portions of a protein structure and optimize ligands within a protein active site, making it useful in conjunction with docking programs.

  • New utility program called FreeForm is available for Szybki users. It provides two distinct functionalities: evaluation of the solvation free energy of the input molecules and free energies of solution conformations. Please Note: FreeForm is not available under 32-bit Windows because of the high memory requirements of this application.
  • A new forcefield for protein-ligand interations is available upon selecting a new option -ff followed by AmberMMFF94 or AmberMMFF94S. It is a combination of MMFF94 (or MMFF94S) with Amber. In this combined force field, MMFF94 (or MMFF94S) is used to describe the intramolecular interactions of the ligand and the Amber force field is used for the VdW and Coulomb interactions between ligand and protein. Currently, this force field can be used only for ligands inside rigid proteins.
  • Entropy estimation based on analytical MMFF Hessian is extended for ligands bound in a rigid protein using the option -entropy.
  • Constraining torsion potential in the form: f8ebfd663514a377a56dfefaeb661230a663dc0f, where 81251f7be3a3c36e3c6602884accebe2d6ab3292 is the user specified force constant and 6b57c4a2f949d360120e9eec70ed44786c71b408 is the reference torsion dihedral angle is available with the use of the input flag -tor_constr.
  • New option -optMethod is introduced for optimization method selection. The possible choices of optimizers type are BFGS, conjugate gradient, steepest descent and mixtures of steepest descent preoptimization followed by BFGS of conjugent gradient. Option -conj is no longer supported.
  • Optimization of molecular systems with large number of degrees of freedom (>= 500) is by default done with the conjugate gradient method unless specifically requested with the option -optMethod.
  • New option -optGeometry is introduced for selection of coordinate system to be used during optimization. It replaces no longer supported options -optcart, -opttorsions, -solid and -noopt. It can be also used to optimize hydrogen atoms positions only, instead of using for that purpose -fixsmarts.
  • Molecules from the input file which failed during processing are by default written to the separate molecular file. See the description of new option -keepFailures.
  • Starting from this release flags -fixsmarts and -harmsmarts are followed by the name of the text file containing a single line with a SMARTS pattern used to fix or constrain atoms. Input of SMARTS strings on the command line for those flags are not used anymore because some SMARTS strings may contain special characters which may be interpreted incorrectly on some platforms.
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