Giovanni Grazioso wrote: > Thanks for your last reply, now the script (concerning the symmetry models) > works well but after a few minutes the calculation ends with the following > message on the log file: > > > pair2___215E> Dynamic memory allocation failed. > Routine, variable, status: icat1
This probably means that your system is very large (spatially). In this case, the default cell-based algorithm for calculating the nonbond list is trying to allocate memory for a huge number of cells, and you're running out of available memory on your system. This may indicate a problem with your input (check the .ini PDB file, to make sure it looks reasonable). Otherwise, short of adding more memory to your machine, you could try setting energy_data.nlogn_use to some large integer to force Modeller to use a "dumb but slow" N*N method to generate the nonbond list rather than the NlogN cell-based method. For example, at the start of your script, add after the 'env=environ()' line:
env.edat.nlogn_use = 9999
See http://salilab.org/modeller/manual/node97.html for further information.
Ben Webb, Modeller Caretaker