geometry optimization output coordinates

Clicked A Few Times	5:57:57 AM PDT - Tue, Oct 22nd 2013 I am attempting to do a geometry optimization and output the optimized coordinates. I use the "xyz" flag, but the coordinate file is not created. The job runs through succesfully; it just doesn't create a coordinate file as I expect it to. My input file is: start md system test noshake solute end basis * library 6-311G* end dft xc b3lyp end qmmm region all density espfit xyz foo_output_coords end task qmmm dft optimize In the end, there are no files with the tag "foo_output_coords". Do I need an additional command to direct it to write out the coordinate file using that tag?

Clicked A Few Times	10:05:42 AM PDT - Tue, Oct 22nd 2013 It will not print xyz coordinates when you do all region optimization. Given, typically, large size of the system in QM/MM runs the xyz option was only meant for region qm. You can always extract PDB file at the end of the run.

Clicked A Few Times	11:06:42 AM PDT - Tue, Oct 22nd 2013 Thank you for your help! What is the best way to extract the PDB file and which file should I extract it from? I know for output from the Molecular Dynamics module, PDB files can be extracted from the trajectory file (*.trj) using the Analysis module. However, no trajectory file is created from the qmmm dft geometry optimization calculation, and it's unclear to me in which output file the final optimized coordinates can be found. If necessary, I can create a PDB formatted file from raw xyz coordinates, if I just knew how to access the coordinates.

Clicked A Few Times	1:11:55 AM PDT - Wed, Oct 23rd 2013 I don't know if it is the faster way, but to extract the optimized geometry I use a prepare module at the end of the input: prepare read file_name_ref.qrs write file_name_opt.pdb end task prepare Ale

Clicked A Few Times	6:06:06 AM PDT - Wed, Oct 23rd 2013 That's great; thank you for your help!

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