AutoDock4.2.6 Part-4 Ligand Preparation

KNP's Pharmaceutical Chemistry
Welcome All
Ligand Preparation Using AutoDock 4.2.6
Links for Complete AutoDock 4.2.6 Tutorials
Part-1: Installation and Preparing your System • AutoDock4.2.6 Part-1 I...
Part-2: Protein Cleaning • AutoDock4.2.6 Part-2 P...
Part-3: Protein Preparation • AutoDock4.2.6 Part-3 P...
Part-4: Ligand Preparation • AutoDock4.2.6 Part-4 L...
Part-5: Generation of Grid Parameter File (GPF) • AutoDock4.2.6 Part-5 G...
Part-6: Generation of Docking Parameter File (DPF) • AutoDock4.2.6 Part-6 G...
Part-7: Running AutoGrid • AutoDock4.2.6 Part-7 R...
Part-8: Running AutoDock Simulations • AutoDock4.2.6 Part-8 R...
Part-9: Analysing and Interpreting Results • AutoDock4.2.6 Part-9 A...

[@claraappiah7461]

Your videos have been very helpful to me. From installation to running the commands. Thank you very much

[@yogeshnegi6424]

Thankyou Sir.......the videos are really very informative and easy to follow

[@KNPPharmaceuticalChemistry]

Thanks and Welcome.
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[@gautamkannan1909]

As soon as I add polar hydrogens to ligand, the autpdpck closes automatically. Please help.

[@KNPPharmaceuticalChemistry]

Thank you for watching our channel.
Try choosing these options - Ligand > Input > Choose > then choose your ligand.
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[@mayankmehendiratta999]

Hello sir liked your all videos related to cadd
I am not able to dock metal complexes in Schrodinger v13.1. Can I have your guidance with regarding to that??

[@KNPPharmaceuticalChemistry]

Thank you for watching our channel.
Will update you soon.
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[@nidhish2701]

Thank you so much for the content Sir.
While preparing the following ligands, It showing error in the 'Torsion tree detection root' step. Instead of highlighting the root carbon, a dialogue- error box (Python) is appearing. Can you please identify the issue and suggest a solution ?
These are the compounds and their smile format,
1. Chloroquine: CCN(CC)CCCC(C)NC1=C2C=CC(=CC2=NC=C1)Cl
2. Cycloguanil: CC1(N=C(N=C(N1C2=CC=C(C=C2)Cl)N)N)C
Thank you for your time and consideration.

[@KNPPharmaceuticalChemistry]

There might be some problem in conversion of ligand to PDB format. once repeat the conversion.
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[@trishachattopadhyay3050]

Sir i am getting an error while trying to add the ligand
IDLE 1.2.2 ==== No Subprocess ====
>>> adding gasteiger charges to mglur_fix
Sorry, there are no Gasteiger parameters available for atom mglur_fix:A: CA807:CA
mglur_fix already has gasteiger charges

[@KNPPharmaceuticalChemistry]

Thank you for watching our channel.
The error message means that your ligand already has gasteiger charges, you can proceed with docking.
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[@FarhanSiddique]

I have ligands containing Zn and Cu (metals) , how can we do docking for that? can you explain

[@KNPPharmaceuticalChemistry]

Thank you for watching video.
Docking of metal complexes or ligands with metals is a complex process in Autodock. one should add the Metal parameters manually.
Will update you soon.
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[@Biswaranjan6373]

At the time of adding Polar H bond it shows error .... Kindly help

[@KNPPharmaceuticalChemistry]

Thank you for watching our channel.
Try choosing these options - Ligand > Input > Choose > then choose your ligand.
Follow for more updates!

[@fozshub4915]

Hello, You didnt use open Babel. What is the use of downloading it?

[@KNPPharmaceuticalChemistry]

Watch this video for more information
th-cam.com/video/LZZcyi5dGSc/w-d-xo.html

[@KNPPharmaceuticalChemistry]

Thank you for watching our channel.
Here is the video to use OpenBable th-cam.com/video/HVKmOyQHuqo/w-d-xo.html
Follow for more updates.