Ceilidh ... Re^3: generating inputs from a large number of geometries

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Re^3: generating inputs from a large number of geometries

Hi Peter!

1. You should put the script somewhere on your PATH, or just in current dir.
2. It is python script. If you running Windows and property installed Python, .py file extension should be registered to be executed by Python interpreter. So, you just need to start command prompt and type format_data.py , (if .py extension is not registered, you need to run c:\path\to\python\python.exe format_data.py)
3,4 If script runs without parameters or with --help parameter (sorry, no GUI) it prints available options. For example, if you want to use def2-TZVP basis set, just run (assuming ahlrichs.lib and input.pdb in the current dir, otherwise provide full paths):
format_data.py -l ahlrichs.lib -b TZVP -i input.pdb -o output.dat

Good luck!
Roman

On Thu Jan 21 '10 10:38pm, P.J.C. Hausoul wrote
-----------------------------------------------
>Hello Roman,

>Thank you very much for the reply. Since I'm new to firefly and related softwares, i've been having a hard time getting firefly to run and now i'm faced with the next problem: i.e. getting the script to run. I had a look at the short explanation that is provided with the link and downloaded installed OpenBabel python module and Python (2.6.4, guessing that the script was written in this version). Then I started to fiddle around in the python shell hoping I could rely on my knowledge of BASIC and VisualBasic. However, after reading several help files, i still fail to see how to use the script and go about my original task. Perhaps i'm missing the point, so I would be very gratefull if you could provide me with a laymans explanation on running the script :

>1. where do i put the format_data.py file and where the ahlrichs.lib?
>(i was going with putting them in the \lib and \libs in the python dir)
>2. which program do i use to run the script ? do in need to use openbabel and python at the same time ?
>3. how do i specify the type of basis sets and ECPs i want to use ?
>4. how do i tell it where the PDB files are and where it should write the converted inputs ?

>Thanks a million.
>Regards Peter

>On Tue Jan 19 '10 11:56pm, Roman Zubatyuk wrote
>-----------------------------------------------
>>Hi Peter!

>>Regards,
>> Roman.
>>
>>
>>On Tue Jan 19 '10 10:57pm, P.J.C. Hausoul wrote
>>-----------------------------------------------
>>>Hello All,

>>>I'm new to this forum and PC-GAMESS/Firely and maybe my question is simple to answer, maybe not, i'll go ahead anyway...

>>>I managed to get firefly running (DFT/B3LYP calc.) in parallel with a hand written input (specifying basis sets and ECP for each atom) However, I have quite a large number of geometries I would like to calculate using a fixed set of parameters (DFT/B3LYP, 6-31G* on H/C/N/O/P etc and LANL2DZ with ECP on Ni/Pd/Pt etc) Therefore is was wondering if it is possible to generate such inputs in an automated way from PDB/XYZ files ? I looked around on the internet for GUIs and related software however these generally lack a simple way of implementing atom specific basissets and ECP. I have also discussed with collegues on this matter and one suggestion was that it may be possible to use external geometry files in combination with external basis set files. Is this possible in Firely and how should i go about this ?

>>>Thanks in advance and regards,

>>>Peter

Fri Jan 22 '10 7:03pm

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