Ceilidh ... Re^8: generating inputs from a large number of geometries

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Re^8: generating inputs from a large number of geometries

Hi Roman,

Sorry to make this such a long thread. I'm sure all the files are there and that the script runs. Interestingly it seems that it will only run using the following command :

format_data.py -l AHLRICHS.LIB -b TZVP input.pdb

Will use AHLRICHS.lib as basis library file
Requested basis set is TZVP
Reading input file input.pdb
Read 50 atoms
Writing output file input.data

If i include the option "-i" i get the following:

format_data.py -l AHLRICHS.lib -b TZVP -i input.pdb

No input file
try 'c:\PDB\format_data.py --help' for more information

So for single files it works fine, but any change to the command line with result in the 'no input' error.
I also tried your suggestions but these gave the same errors.

Regards Peter

On Sat Jan 23 '10 5:08pm, Roman Zubatyuk wrote
----------------------------------------------
>well, this simply means that "file not found". are you sure, that input file exists?
>could you post exact output of the commands:
>dir ahlrichs.lib
>dir input.pdb
>format_data.py -l ahlrichs.lib -i input.pdb -b tzvp -o output.dat
>
>On Sat Jan 23 '10 1:47pm, P.J.C. Hausoul wrote
>----------------------------------------------
>>Hello Roman,

>>I tried the command line exactly (correcting fomtat to format), but still i get the same error message

>>regards Peter

>>On Sat Jan 23 '10 4:30am, Roman Zubatyuk wrote
>>----------------------------------------------
>>>The simplest command line to process files in a batch in Windows:
>>>for %f in (*.pdb) do fomtat_data.py -l ahlrichs.lib -b TZVP -i %f -o %~nf.dat

>>>On Fri Jan 22 '10 11:04pm, P.J.C. Hausoul wrote
>>>-----------------------------------------------
>>>>Hello Roman,

>>>>Excuse my ignorance and thanks very much for the reply. Now its alot more clear. I read the help and did some trail runs and succeeded to convert single files. Nevertheless, I am unable to convert files in a batch fashion. I tried command lines such as:

>>>>format_data.py --inputformat=pdb

>>>>This results in an error message saying the file is not found. Is there anything else I can try or is the script limited to converting single files ?

>>>>Regards Peter

>>>>On Fri Jan 22 '10 7:03pm, Roman Zubatyuk wrote
>>>>----------------------------------------------
>>>>>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

[ This message was edited on Sat Jan 23 '10 at 9:26pm by the author ]

Sat Jan 23 '10 9:26pm

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