Answer for during the docking of Sn compound by Autodock vina, i am facing this error "AutoDock Vina throws an error with the following message: ATOM syntax incorrect: "Sn" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive"
Hi, Try adding these coordinates in the param file: atom_par Pt 2.75…
Answer for Error at equilibration step, unable to access the topol.top file
Hi, It's difficult to understand your issue. Can you please provide a…
Answer for Value Error: Zero size array while running POVME 3.0
Hi Sunidhi, Thank you for reaching out. Can you tell me at…
Answer for problem-in-launching-autodock-tools-from-ubuntu
Kindly go through the following article. It is explained in detail how…
Answer for Error in using the make command on terminal Charmm installation
Hi, Try the following commands: sudo apt install g++-10 sudo apt install…
Answer for pdbqt files preparation for Vina
Yes, there are some python scripts but the problem is how would…
Answer for query in topology prepartion
Hi, Please see the following tutorial: https://bioinformaticsreview.com/20200712/tutorial-md-simulation-of-a-protein-ligand-complex-using-gromacs/
Answer for tools or software for computational prediction of transcription factor cluster binding sites
Hi, Read the following article: https://bioinformaticsreview.com/20210420/most-widely-used-tools-for-transcription-factor-binding-site-prediction/ Best
Answer for Autodock Vina
Hi, Try using Autodock4Zn. Otherwise, Vina can easily recognize metal ions in…
Answer for Error: Could not open file “protein.pdbqt” for reading
Make sure you have named your protein file as “protein.pdbqt” else change…
Answer for Error: Could not open file ligands.txt
Make sure you have named your ligand names file as "ligands.txt". Check…
Answer for How do I define ligand names for virtual screening?
The ligand names for virtual screening are defined in a separate file,…
Answer for How to know binding pocket of a predicted structure of a protein for VS?
Hi, You can predict binding sites using the CASTp server and any…