Hi to all, I'm doing protein-liagnd interaction using DS v2.5. I got the pdb file of protein, cleaned the water, added the hydrogen, defined as receptor, and formed the cavities. Everything is OK up to now. Then I opened the ligand file(sd form), run the LibDock protocol, but it failed. the report said that 'Ligagnd failed conformer generation'. Even when I used the samples given by DS, it failed with the same reason. I don't know how to deal with it.
Another question is that when I run the prepare ligand protocol, it also failed. One line in the failed file denoted '3D failure'
Hi Yang,
In our lab we have DS version 4.1. but it would work same for version 2.5.
Firstly does you sd file import in DS main window indicating 3d structure or 2d structure? i guess, it would be in 2d structure. if it is so, then you have to generate 3d conformation for ligands. this can be done by using clean geometry after adding hydrogen to the ligand.
Dear Tanuj,
Thank you for your anwser! I have tried it again but it failed with the same reason.
The ligands was originally drawn by myself using Discovery Studio Visualizer 2016. I opened it in DSV and add the poler hydrogen, then I click the 'clean geometry'. After that, I save it as the sd form. Then I opened the receptor protein and the ligands file in DS v2.5 and it failed again.
The files I upload is the receptor and the ligands. May you try to run it in your lab if you have time? I'm wondering if the problem roots in the adaptation between my computor and the softwore.
Thank you again!
Hi Yang,
sorry for late reply, as we had some network problems.
i carried out the libdocking of your .sd file with receptor, and it completed successfully.
firstly, i converted your .sd file to .sdf file format. Then, i prepared the protein with protein preparation wizard. After that i simply performed the docking using libdocker module.
i browsed the path of ligands .sdf file and used default set to check weather the protocol will perform the docking or not.
it performed the docking. I think, may be the libdocker license is not configured.
regards
Tanuj
Dear Tanuj
Sorry for late reply, since I was busy dealing with my courses these days.
Thank you very much for your kind help! I will try to figure out what's wrong with my software.
Thank you again!
Regards!
Yang
- Badges
- Science topic
- Similar topics
- Chemistry
- Pharmacology
- Pharmaceuticals
- Drugs