Research:Typer

Program Overview

• Electrostatic parameters
  • Gaussian fchk as input
  • MOPAC2007 ESP on the grid,then fit -- is the speed much better? accuracy?
  • transfer from fragment databases? how to merge? (bond increment) accuracy?

• vdw and bond, angle, torsion, out of plane
  • typer (databases growth?)
  • refit torsion as required (if use input the profile)

• Output
  • tinker key file
  • amber topology

• standalone or web server

Poltype setup on Ren lab cluster

• Using bash shell:

source /home/wuch/gaussian-setup/.g09.bashrc
export PYTHONPATH=$PYTHONPATH:/opt/software/CHEM/openbabel-2.2.3/lib/python2.5/site-packages
export LD_LIBRARY_PATH=/opt/software/CHEM/openbabel-2.2.3/lib:$LD_LIBRARY_PATH

• Using csh/tcsh:

source /home/wuch/gaussian-setup/.g09.cshrc
setenv PYTHONPATH $PYTHONPATH:/opt/software/CHEM/openbabel-2.2.3/lib/python2.5/site-packages
setenv LD_LIBRARY_PATH=/opt/software/CHEM/openbabel-2.2.3/lib:$LD_LIBRARY_PATH

Advanced SDF specifications

• Available here: /opt/reprints/individuals/wuch/booksctfile.pdf

Miscelaneous

Phenol Multipole Test

Site 1	Site 2	Norm
4	6	0.0165
3	7	0.1181
4	7	0.1335
6	7	0.1347
3	4	0.1675
3	6	0.1727

special cases

bisector and non-chiral Dx Dy, Qxy, Qxz, Qyz =0