SZYBKI 1.7.0

New features

  • An extension of the MMFF94 force field for three coordinated boron compounds is offered in this release. Most compounds containing B-X bonds where X=C,N,O,S, and H are covered with the following exceptions: X=N(imine),N(sulfonamide), N(pyridinium) and N(quaternary). Also not supported are compounds in which boron is bonded to X=F,Cl,Br,I,B and Si, or makes a bond angle BYX. Compounds in which boron is a part of four-membered rings of B1CCC1 type are also not available in the current parameterization because their existence is questionable: Ab initio calculations at the MP2/6-31G** level failed to identify stable structures for them (highly polar structures in which boron is four-coordinated are formed).

  • New input flag -solv_dielectric is added. It controls solvent dielectric for all PB and Sheffield calculations. Default value is 80. Flag -prot_dielectric is changed into -inner_dielectric. Previous flag -prot_dielectric can be used.

  • New option flag -salt x which sets the salt concentration for PB calculations is added. x is concentration in mM. Default value is 0.

  • New option -flex_file which allow to specify only those atoms which will be optimized is added.

  • Starting from the current release, binding entropy (\(T\Delta S\)), can be calculated in a single run:

    szybki -entropy QN -complex pl_complex.oeb -ligands ligands.oeb

    where pl_complex.oeb is a protein-ligand complex file, and ligands.oeb contains an ensemble of ligand conformations in solution.

  • Entropy calculation of protein-bound ligands has been modified. Specifically, the fraction \(f\) of ligand surface exposed to the solvent used in the entropy component term: \(f\Delta S_s\), is calculated currently as \(f = A_{Lexp}/A_L\), where \(A_{Lexp}\) and \(A_L\) are ligand solvent accessible surfaces in the protein complex and solution respectively. The reason for a change is the recent OpenEye internal study which show that the above fraction \(f\) calculated according to the equation: \(f = 0.5(A_L - A_P + A_{PL})/A_L\) ([Wlodek-2010]) is for many protein-ligand complexes overestimated.

  • The default value of microscopic surface tension used for protein entropy desolvation calculation is now 6 \(cal/(mol A^2)\) (previously default value was set at 5 \(cal/(mol A^2)\). The flag -sfp x, where x is microscopic surface tension for protein desolvation entropy calculation, allows to overwrite the default value.

  • Two more flags have been introduced: -t x and -rws. The first of them sets the temperature x in C for entropy calculations (the default value is 25C). The second flag removes water molecules from all solvent accessible surface calculations used for the evaluation of protein-bound ligand entropy, in the case the input protein contains water molecules.

  • More entropy terms are reported in the log file. In earlier SZYBKI versions only the total entropy was reported. Starting from 1.7.0 release in addition to total entropy, configurational, solvation (or partial solvation) and protein desolvation entropy terms are reported.

  • flag -mol2charges is replaced with -current_charges. -mol2charges is now an alias to the new flag.

  • The format of the log file has been changed. Its readability is significantly improved.

  • A new option -out_complex is added. It allows to output a protein-ligand complex after ligand optimization in partially flexible protein.

Bug fixes

  • Optimization of polar hydrogens with the -polarH option when the input protein was in the PDB format resulted occasionally in mangling PDB atom names in the protein output file. This bug has been fixed.
  • Combination of flags -complex, -protein_elec PB and -exact_vdw caused a crash on Windows platform. This bug has been fixed.
  • Previous Szybki versions produced the parameter and status files even when Szybki was run without any user option. This problem has been fixed in the current release.
  • Optimization of ligands in the partially flexible protein receptors in the case when the input file contained more than one ligand, stopped after processing the first ligand. This bug has been fixed.
  • Information on the selected user options was written to the stdout. That was making piping impossible. This behavior has been eliminated in the current release.
  • Input molecular files with badly specified geometry (with atom clashes), were not handled properly. Starting from the current release such an input is caught and the processing of such a molecule is skipped.
  • Optimization of large molecules (e.g. optimization of hydrogen positions in very large proteins) can lead to memory exhaustion on some platforms, due to too large amount of VdW interactions or inability to allocate Hessian matrix in the quasi-Newton optimization. Previous Szybki releases terminated on such cases with the bad_alloc crash. This has been corrected by terminating the run and generating information on the mentioned above cases, so the user might decrease the number of VdW interactions or switch to conjugate gradient optimization method.