How can I calculate binding free energy between protein and ligand complex after running protein_ligand complex md simulation?

More Sunidhi Bhatt's questions See All

Unexpected 35 kDa Band Observed During Expression and Purification of Dengue 3 NS5 RdRp Domain ?

Background: I am developing an RdRp assay for Dengue virus-3 and need to express and isolate the NS5 protein's RdRp domain (~101 kDa). My expression vector includes a GST tag followed by a 6x His...

13 July 2024 9,950 3 View

How is artificial intelligence being utilized to enhance the diagnosis and treatment of sleep apnea?

AI has the potential to improve the management of sleep apnea by personalizing treatment, enhancing diagnostic accuracy, and advancing our understanding of the condition.

03 July 2024 9,393 2 View

How to dilute my DNA Template( 1 Micromolar stock solution ) into1 × 10-8 nM to 1 × 10-15 nM ?

How can i dilute my master stock of 1 micromolar DNA template to different concentration by serial dilution

17 May 2024 3,641 2 View

Why can't Ansys HFSS be used for LiDAR Based Simulation?

Hey All, I am currently trying to simulate an FMCW Lidar in Ansys HFSS which I used for RADAR Simulation and I cannot find a way out to perform Lidar based simulation. If anybody knows how to do...

20 March 2024 2,749 2 View

Hi, A phospholipid qualitative analysis is to be performed in liposomal formultations.Is HPLS-UV a reliable technique for same ?

A phospholipid content has to be estimated in liposomal formulations.Is HPLC-UV a reliable technique for same or should other techniques be employed?Which one is the most suitable of them all ?

22 November 2023 4,883 1 View

How to generate ligand.itp and ligand.gro files for md simulation using amber14 force field?

How to generate ligand.itp and ligand.gro files for md simulation using amber14 force field?? Kindly help!! Thanks in advance.

12 November 2023 2,434 4 View

Where I can do extrusion of Magnesium alloy in india?

Any vendor or Institute.

05 November 2023 3,030 0 View

Error while generating ligand topology?

I'm trying to generate ligand topology files through CHARMM FF but i'm getting this error. I installed the respective python version but error is still same python cgenff_charmm2gmx.py UNK...

23 October 2023 1,587 4 View

How can I insert a protein structure model within Lipid bilayer structure model?

How can I insert a protein structure model within the Lipid bilayer structure model? Kindly help.

12 May 2023 5,082 3 View

What are the alternate servers for PRODRG to generate ligand topology? I have tried ATB, ACPYPE also but ligand gets detached from the protein?

what are the alternate servers for PRODRG to generate ligand topology? I have tried ATB, ACPYPE also but ligand gets detached from the protein while generation complex.gro file in the MD run....

23 April 2023 7,765 3 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 3,588 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

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

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

Not able to give GAFF forcefield to my ligand?

I have been able to assign the CHARMM forcefield to my ligand i.e. acetyl coenzyme A but not the amber forcefield. I want to run amber forcefield and the parameterization of ligand is failing. I...

15 July 2024 7,323 1 View

Printing residues in an object in Pymol?

Hi! I am currently working on a protein where I have selected residues within 10A of its bound ligand in pymol. However, I can not find a way to print out what residues are contained in that group...

15 July 2024 1,727 1 View

How can we identify (in silico) the interacting amino acid residues or the nucleotides involved in the Protein-Protein / Protein-RNA interaction?

Hello! everyone, I am trying to study in silico Protein-Protein and Protein-RNA interactions. Now, is there any tool with which I can identify the interacting amino acid residues or the...

14 July 2024 950 2 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 I use different force field for protein and ligand?

Hello, Dear! Generally, I used CHARMM36 + cgenff force field for simulaiton. But,, due to certain parts of lignad, force field cannot be generated using Cgenff. Can I use different force field...

10 July 2024 9,513 3 View