How do I dock two ligands?

31 July 2013 1 8K Report

Is it possible to dock two different ligands with Autodock or is there other software to attach ligands? I have tried with chemsketch 12.0 but there is no proper coordinates while converting to pdb format. Any suggestions?

Uttam Pal

Use ChemDraw 3D or Avogadro (http://avogadro.openmolecules.net/wiki/Main_Page). Avogadro is free.

You can dock two ligands in AutoDock but not in one step.

Badges
Science topic

More K. Gowri Shankar's questions See All

How to increase simulation box size?

We intend to study the interaction between peptides and polymer (like PP, PE and PS) through MD simulations using Martini force fields ( Martini 2 for PP and Martini 3 for PE, PS). We have...

08 August 2024 4,842 0 View

How to prepare the nanoparticle treated fungal sample for Environmental SEM analysis?

A fungal strain was treated with nanoparticles. We want to do an environmental SEM analysis. So could anyone share your views on preparing the sample? Thank you.

07 August 2024 5,307 1 View

How to decrease hydrophobicity of Ni-foam?

As, my studies are related to water adsorption, the substrates should be hydrophilic in nature. Ni-foam being hydrophobic in nature, the results are not as expected as in literature. Hence i...

14 July 2024 8,847 4 View

Is VSM measurment of NdFeB alloy powder sample require any spesific sample preparation ?

Is any specific sample preparation required to perform VSM measurement of NdFeB alloy powder to get a square-shaped M-H loop? Or is it mandatory to make magnetically aligned and sintered pellets...

09 July 2024 1,969 0 View

How to see whether my protein is aggregated using western blotting?

I am working on one protein which gets aggregated (similar to alpha-synuclein and tau) in certain neurodegenerative diseases. I am trying to confirm the aggregation using Western blotting....

30 June 2024 5,060 3 View

How can i calculate the band alignmet of Sc2CO2/BlueP heterostructure from DFT?

I know the work function and band gap of each monolayer and heterostructure. I calculated mulliken electronegativity(X) of Sc2CO2 and Bluep. From that i found Ev = X- 4.5+Eg Ec = Ev-Eg, where Eg...

28 June 2024 9,360 0 View

Can anybody tell me how to find out the ionic concentration of influent (Ci) and effluent (Co) water?

I'm performing CDI experiments wherein to find deionization rate i need to know the ionic concentration of influent and effluent. Can anybody please explain how to find?

19 June 2024 5,572 12 View

How to get Consistency Ratio when scale of relative importance is used in AHP?

In AHP (Analytical Hierarchical Process) using 9 criteria, when I use a a scale of relative importance (1-9), I am getting a higher lambda-max and hence an inconsistent Consistency Ratio (>.10)...

16 June 2024 1,228 1 View

Can we use any inferential statistics on a data set measured using non-validated questionnaires?

I have heard from my senior scholars that we can't use a non-validated scale to measure variables in a correlational study. Is it true? Can anyone help me with finding a reference for the same.

05 June 2024 7,851 4 View

How to get 2 Octanol from Castor oil at a laboratory scale ?

Any latest method developed

24 May 2024 2,128 1 View

How can I prepare virus for a TEM or SEM imaging?

I have virus (viral hemorrhagic septicemia virus) in suspension and the experiment will not involve cells. What level of TCID50 is preferred?

11 August 2024 3,115 1 View

Handling Missing Data and Building a Predictive Model with Incomplete Information ?

I am developing a predictive model for a water supply network that involves 20 influencing points. However, I only have historical data for 10 out of these 20 points. I would like to know how to...

10 August 2024 4,005 2 View

Which Scopus Journal provides the most affordable fees?

"PUBLISHING IN A SCOPUS JOURNAL" Researchers are now at a cross road. The critical need to publish in a Scopus or ISI, etc journal is ever vital. Journal Publication fees must be submitted....

10 August 2024 8,621 1 View

Seeking Advice on Viability and Execution of Undergraduate Thesis Topic?

Hello everyone, I am currently developing a thesis proposal and would appreciate your input on its viability and how to effectively carry it out. My proposed topic is: "Does the perceived threat...

10 August 2024 8,992 0 View

Is it possible to use the Fused Deposition Modeling (FDM) to additively manufacture interconnected porous structure generation of >100-200 micrometer?

Usually, additive manufacturing techniques like SEBM, SLS, and SLM are used for interconnected porous lattice structure generation with sizes of >100–200 micrometers. Can the Fused Deposition...

09 August 2024 7,892 0 View

How to define an anisotropic material with asymmetric elastic compliance/stiffness matrix in ANSYS APDL?

I need to model an anisotropic material in which the Poisson's ratio ν_12 ≠ ν_21 and so on. Therefore, the elastic compliance matrix wouldn't be a symmetric one. In ANSYS APDL, for TB,ANEL...

09 August 2024 5,048 2 View

Who will be moral responsible for the death of thousands of people in the event of an earthquake?

Who will bear moral responsibility for the deaths of thousands of people in the event of an earthquake? Weeks and months remain before the onset of strong earthquakes that bring death to...

08 August 2024 6,134 12 View

GC-MS retention index prediticon?

Hello experts, Does anyone know any free software about retention index prediction ?

08 August 2024 7,403 2 View

How can I apply boundary conditions in an orthotropic steel deck numerical model using ABAQUS software?

I am trying to simulate vehicular loading on an orthotopic steel deck bridge section in ABAQUS software. The red arrow mark in the attached figure indicates the direction in which the vehicle will...

08 August 2024 719 0 View

Can you suggest reliable sources defining "3D mesh" and "3D city models"?

Dear fellow researchers, I am currently working on a paper where I need to provide a reliable reference that defines and distinguishes between 3D mesh models and 3D city models. Although I am...

06 August 2024 9,986 2 View