I am trying to dock my protein.pdb and ligand.pdb generated from different PDB files. Each of them have only one molecule (Mol A for protein.pdb and another Mol A for ligand.pdb).
Is there any way to dock these two objects together using YASARA. I tried to follow the general macros mentioned in the manual of YASARA but it just does not work. Here is a screenshot of the error.
Thank you.
Dear Thai Leong Lai,
the macro you are using (i guess its 'dock_run.mcr) only accepts YASARA Object (yob) or pdb files (in the macro the line is: "for type in 'yob','pdb','sdf'"). From you screenshot it's obvious that you used a .mol2 file. You first should convert both structures (you can do that in YASARA) into .pdb or .yob format.
Best regards
Johann
Dear Dr Johann,
Thank you for your answer. You are right, I was using dock_run.mcr.
I actually tried various as my target but there's no .mol2 file in my memory, which was why I found this error to be odd. I only set either, .sce, .yob or .pdb in each of my previous troubleshooting attempts.
Attached are some of the files I used. Are there any errors?
I look forward to hearing from you. Thank you!
Best regards
Thai Leong
Dear Thai Leong,
first, it looks like that even .mol2 files should have caused problems, because they are included in the macro in newer Yasara versions. Sorry for that! I was not up to date on my notebook.
I guess your problem might most likely be that you chose the wrong 'MacroTarget'. From the screenshot I remember that this was a lengthy name including this .mol2, right? But according to the files you sent me, the Macrotarget should be "3U1JOri". The macro then adds "_receptor" and "_ligand" as well as the file ending to it.
I hope that helps!
Best wishes
Johann
Dear Dr Johann,
Thank you for your answer.
Unfortunately. it still does not work. The YASARA software is already updated and I do not know why does the error happen.
Best wishes
Thai Leong
Dear Thai Leong,
if you send me a "protocol" of the full procedure (including in which (sub)directories your files are located) you do when getting the error I can have a closer look at it!
Best wishes
Johann
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