I checked the ADFR tutorial with my own files and it works fines. ADFR could predict the binding site and the first suggested pocket was the protein active site. This's a great tool; however, as you described in this tutorial, the developers were not engaged in details to provide users with detailed documentations on how users can run this tool.
Great video! One thing that I was confused by was where you acquired the crystallised ligand from. And also, would I be correct in observing that in the cmd line for docking the reference ligand as well as the docking ligand were the same molecules?
First, the crystallized ligand was a single file with the receptor, PDB 6LU7. Before the video I separated them. Second, for this example, you are correct. I docked the crystallized ligand and compared the result to the know crystal structure. This is a positive control. I hope I've answer your questions.
Yes. First, check if ADFR is M2 compatible. Second, if it is now compatible, get and Intel- or AMD-based computer and run ADFR there. Third, configure the ssh server on that machine. Fourth, connect from you2 M2 MacBook Air to the remote computer and run your docking.
Hello , when I ran the ADC to dock peptides in final step of docking I got the different result from what is described but I use the same file as shown. is there any solution for this ?
Meet, if you did everything exactly as I did you cannot get the same results exactly. Most docking software use a random seed. Some allow the user not to. In ADFR case, the use of the flag -S would force a -1 seed. For anybody to always get the same results for the same docking every single time, the use of -S is necessary. If you carried out the process differently I cannot know what you did. I also mentioned that I had prepare my receptor before the docking. Thus, your receptor preparation might be different. Since you do not specify what came out differently, this is my best answer.
Actually I want to dock peptide to protein and I use ADCP for it. In which as mentioned in procedure first I use (reduce package ) to do protonation of ligand and peptide and then receptor and ligand preparation , then I made up Target file for docking which has the same result as mentioned in procedure and at the end of docking I got some lower Binding energy compare to result. If possible please mention your mail I'd so that I can send you result
Thank you for such beneficial video. what about the flexible receptor docking? Nowadays, I have been trying to perform a induced fit docking by Autodock FR, by selecting certain flexible residues on my receptor. But I couldn't succeed for now. Could you advise sources/tutorials about this.
Hello, it is great suggestion. There are two ways to go about it with ADFR. Using agfrgui, which is kinda tricky. The other one is using agfr in the command line. It is not difficult to do but selecting the right residues might be the limiting step. Stay tuned and I´ll try to produce something.
Ok, let's start by saying: autodock4 instructions should work. No, let's drop to the instructions. Word of caution: I haven't tested this. From what I can gather ADFR has its own AD4.1_bound.dat. In my system it is located in the installation folder: ADFR/CCSBpckgs/ADFR/Data/AD4.1_bound.dat I think that if you edit this file as describe here: autodock.scripps.edu/how-to-add-new-atom-types-to-the-autodock-force-field/ you should be able to add parameters. Try it. Make sure you backup the original file first, alright? Good luck.
I checked the ADFR tutorial with my own files and it works fines. ADFR could predict the binding site and the first suggested pocket was the protein active site. This's a great tool; however, as you described in this tutorial, the developers were not engaged in details to provide users with detailed documentations on how users can run this tool.
Great video! One thing that I was confused by was where you acquired the crystallised ligand from. And also, would I be correct in observing that in the cmd line for docking the reference ligand as well as the docking ligand were the same molecules?
First, the crystallized ligand was a single file with the receptor, PDB 6LU7. Before the video I separated them. Second, for this example, you are correct. I docked the crystallized ligand and compared the result to the know crystal structure. This is a positive control. I hope I've answer your questions.
I am getting "zsh: segmentation fault" when I am trying to open agfrgui on M2 macbook air. do you have any suggestions?
Yes.
First, check if ADFR is M2 compatible.
Second, if it is now compatible, get and Intel- or AMD-based computer and run ADFR there.
Third, configure the ssh server on that machine.
Fourth, connect from you2 M2 MacBook Air to the remote computer and run your docking.
Hello , when I ran the ADC to dock peptides in final step of docking I got the different result from what is described but I use the same file as shown. is there any solution for this ?
Meet, if you did everything exactly as I did you cannot get the same results exactly. Most docking software use a random seed. Some allow the user not to. In ADFR case, the use of the flag -S would force a -1 seed. For anybody to always get the same results for the same docking every single time, the use of -S is necessary.
If you carried out the process differently I cannot know what you did.
I also mentioned that I had prepare my receptor before the docking. Thus, your receptor preparation might be different.
Since you do not specify what came out differently, this is my best answer.
Actually I want to dock peptide to protein and I use ADCP for it. In which as mentioned in procedure first I use (reduce package ) to do protonation of ligand and peptide and then receptor and ligand preparation , then I made up Target file for docking which has the same result as mentioned in procedure and at the end of docking I got some lower Binding energy compare to result. If possible please mention your mail I'd so that I can send you result
@@meetparmar7347 Sorry but no. Maybe at some point in the future.
Thank you for such beneficial video. what about the flexible receptor docking? Nowadays, I have been trying to perform a induced fit docking by Autodock FR, by selecting certain flexible residues on my receptor. But I couldn't succeed for now. Could you advise sources/tutorials about this.
Hello, it is great suggestion. There are two ways to go about it with ADFR. Using agfrgui, which is kinda tricky. The other one is using agfr in the command line. It is not difficult to do but selecting the right residues might be the limiting step. Stay tuned and I´ll try to produce something.
Hello sir, do you know how to add parameters in library with AGFR? The instructions I saw online is for AutoDock 4 only.
Ok, let's start by saying: autodock4 instructions should work. No, let's drop to the instructions. Word of caution: I haven't tested this. From what I can gather ADFR has its own AD4.1_bound.dat. In my system it is located in the installation folder: ADFR/CCSBpckgs/ADFR/Data/AD4.1_bound.dat
I think that if you edit this file as describe here: autodock.scripps.edu/how-to-add-new-atom-types-to-the-autodock-force-field/
you should be able to add parameters. Try it. Make sure you backup the original file first, alright?
Good luck.
Can i get your Emai. I have some questions regarding that
No private consults, only through this comments. Cheers.