Why does my ligand pdbqt is not being found by the auto dock vina?

More Thilothamai Jegani Kannan's questions See All

What can be the minimum number of animals (rats) to be used for a pilot/preliminary study on intradermal drug delivery?

Dear All I would like to know the minimum number of animals (rats) to be studied for a pilot/preliminary research on intradermal drug delivery. Can I proceed with 1 animal per group for a pilot work?

02 August 2024 4,570 1 View

Can anyone suggest me the questionnaire along with scoring key to assess the mental health wellbeing of the college faculty?

I am Ruthra, and I have been working as a psychologist for the past 10 years. Now, I'm interested in conducting research and I would like to conduct a survey on mental health and wellbeing among...

15 July 2024 4,119 4 View

Is PyMOL available in github free or not ?

Can someone clarify whether the Pymol version is available in GitHub free or to be subscribed to? Can this Pymol be installed in Python and be used for research publications ? I installed Pymol...

12 June 2024 9,969 2 View

Is there any fibonacci number F_k such that n^2+n = F_k for any integer n other than 0 and 1?

That is product of two consecutive integers is a Fibonacci number and hence it must be even.

24 March 2024 1,912 4 View

What are the options for distant PhD in public health specialities for a medical graduate? Are there suggestions for Universities? Please suggest?

PhD University suggestions are welcome from across the world.

13 March 2024 1,508 7 View

What could be the reason to get different band intensity when same primers are used for the amplification of the same inserts in different vectors?

Vector 1 (Insert 1, Insert 2, Insert a ) and Vector 2 ( Insert 1, Insert 2, Insert b) contain three inserts in which only the Insert a and b are different. These two vectors are constructed by...

22 January 2024 2,759 4 View

Quantification of Plot profile data in ImageJ?

Hi all, I have the plot profile in imageJ and I saved the data (Distance_(microns) & Gray_Value) for the analysis. Could you please suggest to me how to do quantification with this? Thank you

03 December 2023 3,361 1 View

How to align pdb files using python scipts via python in jupyter notbook ?

I want to cluster multiple pdb files with respect to one reference pdb. I have to use Align > all this to *Ca in Pymol. However, how could i do this via scripting in Pymol? As I have multiple...

15 October 2023 10,053 3 View

How to show two peptide structures side by side on Pymol..?

How to show two peptide structures side by side on Pymol. I have 100 PDB files. I want to show all the 3D image structures side side in a two-dimensional array form. How could I do the same in Pymol?

14 October 2023 8,195 6 View

Reverse osmosis plant water quality issues?

Dears, For each start-up of the skids, our seawater reverse osmosis plant is experiencing some problems with the quality of the permeate water. Conductivity is extremely high at each skid startup,...

05 September 2023 5,481 1 View

Why don't d-orbitals split themselves, why does it take a ligand? why don't protons from ligand repel nucleus split d-orbitals?

why don't d-orbitals split themselves because of themselves without the presence of ligands? Electrons are indistinguishable. Why wouldn't it be more correct that protons from a ligand split the...

03 August 2024 3,589 3 View

Why doesn't chromium 2+ ion use all its d-orbitals to receive lone pairs from six waters in [Cr(H20)6)]3+?

I'm guessing it's because the ligand experiences too much electron repulsion or proton repulsion from the chromium to insert them close to the 3d-orbitals which are close to the metal nucleus. Is...

03 August 2024 1,370 1 View

Can anyone provide me with molecular docking softwares/ websites?

Molecular docking software/ websites?

02 August 2024 8,704 7 View

How can you draw a coordinate bond between a metal and donor atom in metal complexes, using discovery studio visulizer software?

Hello,, The metal complex ligand appears incomplete in the screen of the discovery studio visualizer

30 July 2024 3,354 1 View

AutoGrid and Autodock 4.2.6 window opens for 1 second then closes and there is no output files?

Good day, I am a student trying to work on Autodock for a project regarding Ligand-DNA interaction so i am quite new to molecular docking. i have followed tutorials and did all the steps...

28 July 2024 2,136 4 View

Is it possible to dock more than one drug in the same active site or pocket of a protein to study synergistic/antagonistic/additive properties?

I wanted to know whether we can observe the synergistic/antagonistic/additive properties of combinations or mixtures of compounds through docking analysis. But during docking preparation any...

28 July 2024 7,413 6 View

What is the main factor involve in higher binding score performing molecular docking?

A molecule shows the -11.6 kcal/mol and second one -8.0 kcal/mol so why molecule (A) revealed higher binding score. Please explain major factor involve in it.

21 July 2024 954 5 View

In silico can we join two ligands for docking....?

I have performed docking of proteins with two ligands, both ligands show affinity. I want to check the effect if we join both ligands and perform docking

20 July 2024 2,653 2 View

How to determine LOD values?

I am performing fluorescence experiments using a ligand to detect metal ions. I want to determine the Lowest Detection Limit (LOD) using the formula LOD = 3σ / K. However, I'm uncertain about...

19 July 2024 1,086 1 View

How to extract binding energy from pv.maegz file without using Schrodinger?

I have conducted virtual screening using Schrödinger on a database of 17,000 molecules. Unfortunately, I cannot use the system with the Schrödinger license at the moment. I am trying to find a way...

18 July 2024 2,881 4 View

Annemarie Honegger

Check where your file is located in your file system compared to the default file path used by your autodock installation and that they are no spelling mistakes in your filenames/command files

Rezi Riadhi Syahdi

Please provide more context or screenshot of your problem. Is it not being found by the Vina environment? or by the Vina searching module?

Thilothamai Jegani Kannan

Rezi Riadhi Syahdi I'm getting the error " error: ligand" in the command prompt i have given the proper path and coding too. is there any chance that my ligand is not properly sequenced or its location path is not defined? i cross-checked with a colleague even then there was the same error

I am sorry I could not apprehend the problem. But one solution I can advise you can use AutoDock Vina integrated in PyRx (Go to their website by google "pyrx sourceforge". In my case, it works pretty well, and there is a free option too that will be perfect for you to try. Please check it out.

Rezi Riadhi Syahdi sure thank you