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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