Daylight Worksheet - PCModels/PCFilters...SHOW HINTS!

PCModels can be used from an XView interface (xvpcmodels) or from the command line (clogp and cmr). These exercises will introduce you to xvpcmodels and teach you how to generate and interpret clogp/cmr values for a test dataset.

1. Calculate clogp and cmr value for dopamine (NCCc1ccc(O)c(O)c1) and compare with results from the last exercise using xvpcmodels.
   • Type in SMILES for dopamine or draw in the structure using Grins

   • Select options for Model, Output and Depict

   • Select Compute

   • Try out various Output options

2. Calculate clogp and cmr values for the SAMPLE.medchem.smi dataset (file is at http://www.daylight.com/meetings/summerschool00/files/data/SAMPLE.medchem.smi).
• Get options for clogp and cmr

  clogp +HELP

  cmr +HELP

• clogp, cmr requires TDT files, so first create a TDT file from the SMILES file

  smi2tdt SAMPLE.medchem.smi SAMPLE.medchem.tdt

• generate clogp, cmr values into the SAMPLE.medchem.tdt file

  clogp SAMPLE.medchem.tdt > SAMPLE.medchemcp.tdt cmr SAMPLE.medchemcp.tdt > SAMPLE.medchemcpcr.tdt

• Interpret error codes in results.

  clogp +PCMODELS_ERRORTEXT

• Interpret error codes in results

  Get list of Error Codes

  cmr +PCMODELS_ERRORTEXT