I am unable to add more than one residue in active site

[cmani87]

I followed the process of Chain:Residue1:Number1; Chain:Residue2:Number2. Also the spelling of Analize results is Analyze

[Valdes-Tresanco-MS]

Thanks for the correction, I hadn't noticed. The residue selection is checked automatically, so it is possible that your notation is not correct or does not exist. Please send me the system and the selection to check it if possible.

[cmani87]

I am cross-checking the system. Please give me some time. I will try with two or three more systems and then confirm. Till now, had verified with two OS. There are four options for residues; Automatic is based on auto ligand and it works well. Residue chain number selection is one of the method used with comma or semicolon Chain:Residue: Number followed by semicolon. It’s allowing for one residue selection. And for box selection, I am not sure how to give the coordinates correctly; from where to pick the x,y,z coordinates and the box dimensions; should I use autodock box coordinates here? Centering on hetero atom haven’t checked till now. I am using 1.6.2 version of the software. Should I downgrade to 1.5.1 and check as well? If so, how to uninstall?

On Mon, 1 Aug 2022 at 06:30, Mario Sergio Valdés Tresanco < @.***> wrote:

Thanks for the correction, I hadn't noticed. The residue selection is checked automatically, so it is possible that your notation is not correct or does not exist. Please send me the system and the selection to check it if possible.

— Reply to this email directly, view it on GitHub https://github.com/Valdes-Tresanco-MS/AMDock-win/issues/16#issuecomment-1200558857, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABJJFEVJCB3OBIVGVHUBLMTVW4OT5ANCNFSM55FSNU6A . You are receiving this because you authored the thread.Message ID: @.***>

[Valdes-Tresanco-MS]

I think you are mixing several different concepts in the search space definition. As described in the manual

• Automatic: AMDock estimates the possible binding sites using AutoLigand, then it does a modified docking on each estimated site to "validate" with the scoring function of the docking program which is the most probable binding site. After that, you can use the complex formed at the most probable site and use it to define specifically where to position the search space to perform molecular docking with the appropriate parameters.
• Center on Residue(s): This method uses a single AutoLigand estimate using the geometric center of the selected residue(s). The residues selection is checked automatically as you type and is enabled only if the selection is correct. This method can fail because it depends on the geometric center being at a position outside the protein.
• Center on Hetero: Can only be used when the receptor you have defined has a heteroatom attached. This selection is the simplest. In addition, you can use it with the complex obtained in Automatic mode.
• Box: Used when you already know explicitly the coordinates and the size to use. In case you want to define it manually, simply define it as x:0, y:0, z:0, then "Define search space", display it using the "Show in PyMOL" button, open the AMDock plugin and edit the coordinates and size to your preference (https://github.com/Valdes-Tresanco-MS/AMDock-win/wiki/5.1-Change-Box-specifications-on-AMDock-PyMol-plugin).

If you use any of the first 3, you don't have to worry about defining the box specifications. If you use the last one, it is because you already know the coordinates and dimensions. In either case, you can change the box specifications by following the instructions listed here.

Let me know if this explication solves your doubts