I am unable to run Autogrid command by cygwin. Is there anybody know the right commands to work in cygwin.
Hi Arwind
If you are running AutoDock4 then
autogrid4 -p parameter_file.gpf -l log_file.glg
I hope this will run
Regards
Hai Arvind,
If you are using AutoDock 4 in windows and in your Cygwin linux environment you should have all possible dependencies properly downloaded and installed and then, if you have given your Cygwin directory path in the path variable properly then the command
"autogrid4 -p parameter_file.gpf -l log_file.glg" will defensively work.
if miss any of these things autodock won't work. The best alternative solution is running a Autodock Vina which is more windows friendly and easy to use. The Autodock Vina also works well on the same principles of Autodock.
All the best
Thanks pruthvi for your answer. I didnt get it as when you say to set environment/path varibale in cygwin.
Hi Arvind,
First u install Cygwin, which are shown in C drive in your computer ,then open and go to home ->shown your name-> click and shown Dock and open this folder and paste software autodock4 and autogrid4.
then after ,
open Cygwin and first command to check dock file is present or not. so first command write
cd dock
Then click enter
after then,
./autogrid4.exe -p x.gpf -l x.glg
where x= compound number or symbole
space before -p and -l
Hai Arvind, sorry for the not so detailed answer. i guess Kamal Ahmed has given a detailed answer will surely solve your problem. The path which i was mentioned in my answer is the same which was described by Kamal Ahmed in his answer.
all the best.
@Rao Gollapudi: Autodock Vina is way better than Autodock due to its simplicity in execution and accuracy in the results.
Dear Negi
I hope this comment finds you in good health and spirit.
For running ADT, you should be following 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 installation of above tools, you can run ADT. Here, I recommend you to following my current protocol for running it:
1- create a workfolder 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!
This current protocol can help you for running ADT. I hope it was useful for you. Please do not hesitate to contact me if you have any further questions. Otherwise, I hope that we can work together successfully again another time.
All the best,
Hassan