Can i add heteroatom parameter in AutoDock Vina?

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How to synthesize Schiff base out of amino acid and aldehyde?

I want to make schiff base from amino acid and aldehyde but I am not getting any precipitation. I tried using methanol and ethanol as solvent and adding KOH to dissolve the amino acid in the...

19 December 2023 9,627 8 View

How to take HPLC of Chlorophyll?

What is the best way for High performance liquid chromatography of chlorophyll? What will be the best solvent concentration?

05 October 2023 9,863 2 View

I need to work on 0.1-05 mg/mL concentrations. Is it okay if I prepare 10mg/mL stock solution and then proceed with serial dilution?

Is 10 mg/mL a reasonable stock solution to start with for 0.1-0.5 mg/mL concentrations?

29 July 2023 7,248 5 View

How do I compute for the dose computation?

for example, the needed dose is 400ug/mL, how will I turn my crude extract into 400 ug/mL? p.s my research is about a-glucosidase activity

12 June 2023 9,445 3 View

How to amplify 5-alpha F'Iq Competent E. coli to a transformation efficiency of 10^7-10^9 for my phage display library ?

I have been trying to amplify NEB 5-alpha F'Iq Competent E. coli for my phage display library and therefore need a high transformation efficiency. The commercial product has a TE of 10^9, but I...

06 January 2023 6,359 4 View

What does a high RMSD value indicate in GROMCS?

I have done a 50 nano second protein simulation using Gromacs and obtained an RMSD value greater than 3 nm. is it ok to proceed with it or is the value incorrect?

26 November 2022 4,864 2 View

What does radius of gyrations plot in GROMACS imply?

I have ran a simulation of a protein structure using Gromos force field and obtained the radius of gyration. Is it mandatory to get a linear plot? How does high or low RoG matters? What it implies...

26 November 2022 8,090 2 View

Energy range in autidock vina?

What is the use of energy range in the config file in autodock vina? What is the normal values?

15 January 2022 7,337 1 View

Ligand Optimization for Docking?

Hi. Is it mandatory to optimise our ligand before docking using Autodock or Autodock vina? I have not received the structure from any database therefore the structure was drawn using Marvin draw...

29 December 2021 5,618 3 View

Application for Research Collaboration/Visiting Professor/Lecturer/ Member of Board of Studies

Respected Sir/Madam, I am Prof. Aby John. I would like to be a part of your esteemed academic/research community as a Visiting Professor/Lecturer/Researcher/Board of Studies member. My area of...

01 January 1970 6,512 2 View

Can anyone provide me with molecular docking softwares/ websites?

Molecular docking software/ websites?

02 August 2024 8,704 7 View

How to add Cr parameter in autodock?

When I run autogrid4 it says: autogrid4: ERROR: Unknown receptor type: "Cr" -- Add parameters for it to the parameter library first! Look forward to your reply.Thank you so much!

29 July 2024 488 0 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 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

How to calculate theoretical Ki from the docking results?

I have used Schrödinger (Glide) for docking

13 July 2024 3,003 1 View

Why Cl atom is not showing in docked comlex of molecule?

During the preparation of a ligand molecule in autodock or openbabel Cl atom is not showing in the .pdbqt file whereas it was present in the pdb and sdf file. Due to this Cl atom is not showing in...

13 July 2024 3,486 6 View

Can we analyse RMSD for peptide-HLA docking and binding affinity for peptide-HLA to TCR docking, in a peptide-HLA-TCR docking ?

In the peptide-HLA-TCR docking process, can we express the result of peptide-HLA docking in RMSD and for peptide-HLA to TCR docking, can results be expressed in binding affinity?

11 July 2024 4,831 0 View