Daylight Worksheet - PCModels/PCFilters

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.
• 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 day1.smi dataset.
• clogp and cmr
• Get options for clogp, cmr
• clogp +HELP
• cmr +HELP
• clogp, cmr requires TDT files, so first create a TDT file from the SMILE file
• smi2tdt day1.smi day1.tdt
• generate clogp, cmr values into the day1.tdt file
• clogp day1.tdt > day1cp.tdt
• Interpret error codes in results.
• clogp +PCMODELS_ERRORTEXT
• cmr day1cp.tdt > day1.tdt
• Interpret error codes in results
• Get list of Error Codes
• cmr +PCMODELS_ERRORTEXT