On 3/18/10 9:51 AM, abdullah ahmed wrote: > 1) I do not get log files after running optimization. I am certain that > it is not a matter of them taking really long to be made because I have > been using Modeller for 3 months now and I have not gotten a log file. I > do however, get "pdb.ini" "pdb.rsr" and "pdb.D000001" (contains info on > maximal shift, energy changes and gradients).

You only get a log file if you use the 'mod9v7' script to run Modeller. If you run it in some other fashion, it will behave like a regular application and output the log to standard output, so you need to redirect it to a file.

e.g. at a Linux command line, the following commands do essentially the same thing:

mod9v7 foo.py mod9v7 - < foo.py > foo.log python foo.py > foo.log

If you are running your Python scripts on a Windows machine by simply double-clicking on them, the output will show up in a window and disappear when Modeller finishes. A better way to run these scripts is from a command line or the Python IDLE environment, so you can inspect the log output when Modeller finishes.

> 2) I have a series of molecules that I would like to apply the same > constraints to, and then optimize. Is there a script I can use to > optimize all the files in one go?

Modeller scripts are simply Python scripts so sure, you could write a simple Python script with a loop in it that runs over all of your molecules.

Ben Webb, Modeller Caretaker