When i tried to dock im windows cmd shows Error: could not open "conf.txt" for reading. I have tried to change the path for cmd e.c.t, but it was not helping. And i tried to change from program file to AutoDock folder also, then too its not working..My system configu is 500GB hard disk, 4GB ram, I5 intel core processor running in windows 7. please do kindly help me with this error. i have attached the picture of the error in cmd and my ligand and receptor with the config file..
thank you.
Hi
Replace "all" by "out" in conf.txt file and run command like given attached image.
Note: Keep your input files in directory in C:\ drive, so that you could call it easily.
thanks sir i have got it done by installing vina separately in C:/ drive...and it can read config file..
Hi, Shankar
You can do it with easy way.
1. Copy your file (protein.pdbqt, ligand.pdbqt, conf.txt) in vina folder
2. Hold left shift and click on "open command widows here"
3. type instruction for docking process in command
Enjoy it.
Dear Shankar
I hope this comment finds you in good health and spirit.
For running ADT, you should be following the next steps:
1- Make sure that if python 2.5 installed on your PC: you can download it from the following URL:
https://www.python.org/download/releases/2.5/
2- install Autodock tools: you can download it at:
http://autodock.scripps.edu/downloads/autodock-4-2-x-installation-on-windows/
3- install mgltools:
http://mgltools.scripps.edu/downloads
After having finished the installation of the above tools, you can run ADT. Here, I recommend you to follow my current protocol for running it:
1- create a work folder for your job and tag it based on your favorite name. (e.g. project)
2- running ADT in start menu in windows:
after running you should set its directory: following these steps:
a) open ADT> File> Preferences>set> Startup Directory (in this section you should put on your workfolder path and set it). for example: “C:\Users\project
3- prepare ligand and protein in ".pdb" format. Notice, you must labeled them by "Ligand" and "Protein" keywords.
after having finished these steps you can run ADT: Well! you should do the below ways:
1- open ADT:
File > Read Molecule> Select Protein File (“.pdb” file)
Then:
Edit > Hydrogens >Add>>>>>> Polar Only >OK
Edit > Hydrogens> Merge Non Polar > Continue (in this step if you see any warning please click on "continue")
then:
Edit > Charges > Add Kolman Charges> Ok
File > Save > Write PDB> >Sort Nodes (Check) > OK > (Overwrite) YES
Well! in the next step you should try prepare the ligand:
Ligand > Input > Open> Select Ligand File (“.pdb” file) > OK
Now repeat above steps and then: (in this section you must add charge to your ligand. So, click on Edit menu and:
Edite> Charges> compute Gasteiger
Ligand > Output > Save as PDBQT
******************************
Now you should be executing AutoGrid4:
For run AutoGrid following the below steps:
1-Grid > Macromole > Choose> Click (Protein) > Select Molecule > OK > save
2-Grid> Set Map types >Choose Ligand> Click (Ligand) > Select Ligand
3-Grid > GridBox> Set the BOX> File > Close Saving Current
4-Grid > Output > Save GPF> grid.gpf> save
5-Run > Run AutoGrid:
a) Select Program Pathname: ‘autogrid4.exe’ (i.e. C:\Program Files (x86) \The Scripps Research Institute\Autodock\4.2.6)
b) Select Parameter Filename: ‘grid.gpf’ (you should select it based on your workfolder path)
c) Launch!
Notice! in this step you must waiting for ADT response. please don't "dismiss" it!
***************************************************************
After having finished above steps following the below ways:
Run ADT:
1)Docking > Macromolecule > Set Rigid filename> Select ‘Protein.pdbqt’ > Open
2-Docking > Ligand > Choose> Click ‘Ligand’ > Select Ligand> Accept
3-Docking > Search Parameters > Genetic Algorithm> Accept
4-Docking > Output > Lamarckian GA> Save file as ‘dock.dpf’
5-Run > Run AutoDock
A) Select Program Pathname: ‘autodock4.exe’ (C:\Program Files (x86)\The Scripps Research Institute\Autodock\4.2.6)
B) Select Parameter Filename: ‘dock.dpf’ (Based on you workfolder path)
C) Launch!
Please wait for finishing and don't dismiss it!!
***********************************************************
Docking result analysis:
1-Analyze > Docking > Open> Select ‘dock.dlg’ > Open >Assign Ligand New Name > OK
2-Analyze > Macromolecule > Choose> Click ‘Protein’ > Select Macromolecule
3- Analyze > Conformations> Play, Ranked By Energy > Click on the ‘&’ Button
4-Set Play Options >Check ‘Build H-Bonds’> View the hydrogen bonds formed > Check ‘Show Info’> View the Interaction Energy > Build Current Write Complex> Save as ‘Result.pdb’ ” Save...
Now you can see all of your docking results!
All the best,
Hassan
Hi K. Gowri Shankar,
I have got the same problem with you.Could you please kindly tell me your solution?
Many thanks
Jing Chang
hey jing chang i think its late but just put all the file ligand + receptor + all vina file vina.exe ,vina_license+vina split in a single folder and save conf as txt format .hopfully this will work for you. if not feel free to ask.thanks
Dear Rutash Kumar i am also facing same problem and as suggested by you copy all the files in vina folder. Further, what would be the command to run the process. kindly guide...
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