Hi all,
I need to extract the optimized geometry data to make a mol2 or PDB file.
For example, I first create a structure model of a small molecule, and then I use HF/6-31G to calculate the single point energy. Then I obtain the output from Gaussian 09. I can use Avogadro to visualize the output optimized structure of the small molecule, and save it as a mol2 file.
However, now I have hundrads of small molecules for calculation, how to use command line tools to extract the last optimized structure models from the Gaussian 09 output file?
Thanks a lot!
Hi Martin,
Thanks a lot.
I realized that the checkpoint file, rather than the output file, of the gaussian calculation may be used to extract the optimized conformation. The newzmat utility of Gaussian 09 may be used to get the pdb file from the chk file.
Mr. Zheng,
If you use GaussView, then when you open your output-file (or log-one) you can save your optimized geometry in the corresponding *.pdb and *.mol2.
If you do not operate with GaussView, then you can use Gabedit (www., it is free of charge). By Gabedit you can perform the same data processing.
GaussFreq and the more recent PyFreq do exactly what you ask for:
http://people.unica.it/massimilianoarca/lang/it/research-activity/development-of-software-of-chemical-interest/gaussfreq-2003/
you can open optimized geometry in molden and save final co-ordinates as xyz format then copy it to your desired file
I have attached a picture which gives a clear picture about extracting the final optimized coordinates.
Go to OpenBabel, this tool allows you to transform almost any file between a wide set of popular formats with many options. Download their program. You may have the GUI and set a batch transformation or use a script on the command line.
try cclib on python, you can make a script to read multiple outputs, later you can call to openbabel for saving mol2 or pdb format
I have developed an application that solves a somewhat related problem. You can download it on the following website:
github.com/ricalmang/chemxls
Basically it recursively analyses a directory and its subdirectories looking for input and output files like (*.xyz, *.gjf, *.com and *.log). Then it creates a spreadsheet with all of the data it collected for these files (e.g.: Thermal energies, last SCF cycle energy, Milliken charges and more). It can also create a text file, for each of the outputs, that is formatted exactly like an *.xyz file and contains the last geometry of your calculation. Then a hyperlink to this file is created inside the spreadsheet. In principle you could just change the extension of this text file to xyz and then convert the resulting xyz file into a mol2 file (I know, somewhat cumbersome).
The advantages of this approach is that it escalates extremely well because it works recursively by default (at least if you find a workaround converting txt to mol2) and it is very easy to use (simple exe file and no installation required) . Just to give you an idea, on my laptop, 7th gen i5, it can process about a thousand log files per minute.
Very easy. Open your output file (.out) with GaussView. Right click on the model, choose Tools--Atom List. Then you can see a table with coordinates in it. Export the data then it is done.
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