How to compile the results of UCSF dock6 and also Autodock vina for a set of more than 1000 molecules?

25 May 2017 1 2K Report

Compiling the results for UCSF Dock 6 and Autodockvina. Since Autodock Vina has created separate directories for all the 1000 molecules.. how can I compile those results.

Yoshinobu Ishikawa

Hi Konka,

You should check the following archive:

https://www.researchgate.net/post/How_to_do_virtual_screening_of_a_library_of_ligands_through_autodock_Vina/1

Badges
Science topic

More Konka Dinesh's questions See All

Sensitivity analyze for crop evapotranspiration (ET0)?

Does anyone know how to perform a sensitivity analysis for crop evapotranspiration ( FAO Penman-Monteith equation) using daily meteorological data?

27 December 2020 9,552 3 View

How do I DERIVE equations for lumped elements (R, L, C) from S-parameters?

I have modeled the lumped element circuit for the 3D structure which has been simulated in HFSS. Now I need to derive the equations for the lumped elements keeping the S-parameters of the...

23 December 2020 172 3 View

No title

For academic writing.

17 December 2020 6,465 5 View

How to get nanocomposite of PEEK with Zirconia ?

Need a lengthy PEEK with Zirconia based nano composite of 180 mm length. Which method is possible? Tried injection molding no proper mix. Solvent casting process is also very costly. Kindly anyone...

13 December 2020 4,329 5 View

Choice of sampling time in discretization of control?

What I understand is while applying continuous control to a continuous-time system in MATLAB simulations, actually the control is being applied in discrete manner inherently due to the nature of...

28 November 2020 1,866 4 View

Simulation of sliding mode control for a maglev system?

I tried to simulate a maglev system with continuous time sliding mode but my simulation is showing error (there is a singularity at one of the integrators). I am attaching the modelling and...

16 November 2020 8,964 7 View

Can anyone suggest is there any way to compare the amount of chattering in 2 approaches of sliding mode control in quantitative way physically ?

Suppose 2 methods are shown to do sliding mode control of a given system. Please tell me if we can compare chattering in both by MATLAB or some other way

16 November 2020 3,251 3 View

On what basis two ceramics to be added in base metal to prepare hybrid metal matrix composites?

I am working on Mg-based metal matrix composites. I added two different types(A&B) with a suitable percentage(1%,2%,3% and 0.5%,1%,1.5%) of ceramics separately using DOE and tested. Now I want...

14 October 2020 2,984 9 View

Where i can get Ti based C94 catalyst ?

Ti based C94 catalyst is required for PBAT synthesis

12 September 2020 7,174 4 View

It is possible implement headonic regression model using apache spark milb?

My concern is to use Headonic regression model for market price index analysis.

10 September 2020 9,466 3 View

Dear all, I was wondering if anyone knows whether MGLtools and Autodock can run on Mac OS?

I have tried to download the 64-bit version of MGLtools however, as many times as I have downloaded and uninstall the programs, an error arises that the app needs to be updated. Thank you.

03 March 2021 5,997 2 View

How can I integrate a routing protocol in a tiny device (e.g. Raspberry Pi)?

Hi Community, I'm facing the issue of integration/compiling a new routing protocol in a WSN simulator. The final goal is to successfully add, configure this routing protocol in hardware devices...

01 March 2021 9,332 6 View

How do I add a udf to Ansys fluent and does it need to be compiled before hand ?

I have a Define_CG_Motion udf written in c where do I add it to my Ansys fluent project and does it need to be compiled before that?

21 February 2021 9,347 3 View

What are the potential shell well and atomic solvation parameters for the boron atom?

I have a protein-ligand docking project. The ligand contains boron atoms that are not detected by Autodock software. To solve this problem, it is necessary to introduce the boron atom to...

19 February 2021 1,236 1 View

How to Remove different version of atom from pdb Crystal Structure for Docking Preparation?

I am new to Docking and MD, and currently try to catch on it. I try one of the webserver for docking, but unfortunately not working. it says " Your PDB contains multiple forms of the same residue...

08 February 2021 7,426 3 View

How do you get around this AutoDock Vina error?

I get the following error messages after running the simulation: Sorry, there are no Gasteiger parameters available for atom ligandx.ligand:A:lig1:O7 AutoDock Vina ligand docking initiated for...

26 January 2021 3,822 3 View

The dimensionality of protein and ligand is reduced after docking?

I used autodock to complete the docking between the ligand and the protein. I have a question, why the dimension of the result after docking is much smaller than the dimension of the protein...

24 January 2021 7,363 3 View

How to generate .dlg files on PyRx?

Hi. I'm using the PyRx version 0.8 and getting the error message: WARNING: Filename mismatch: "2DFN_ADP_CL.maps.fld" :: "..\2DFN_ADP_CL.maps.fld" C:\Program Files (x86)\The Scripps Research...

17 January 2021 843 3 View

Servers for finding free energy and dissociation constant of protein-protein docked complex?

Hello everyone, I would like to get help about finding any server or application which can give me info about free energy and dissociation constant of protein-protein docking outputs. I have...

15 January 2021 587 3 View

What would be the best option to dock a number of peptides to a protein?

I have been using PyRx to dock peptides to a protein. Initially the numbers were small so it was okay. But now I have to dock over 500 peptides and doing so manually would take forever. My...

10 January 2021 3,330 4 View