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

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What if top fiber concrete strain exceeds the ultimate strain when fixing the yield strain in steel i.e to calculate yield moment in circular column?

I have prepared an excel sheet to calculate yield moment and curvature for a hollow circular section. In which Depth of Neutral Axis is fixed using "GOAK SEEK" function. Axial Force is input of...

22 November 2020 4,632 3 View

How to do MD simulation of docked protein complex after docking .?

I have perform some protein-protein docking studies. I used Hdock, Prizm. But I am unable to find a proper method to verify my docked structure. I also docked my structure in Hex program to get...

19 October 2020 4,083 7 View

I want to know about command to fetch XTC and PDB file For markov Calculation?

I am learning markov state model in jupyter notebook. When I am fetching data with mdshare.fetch() command from tutorial its okay. But how I will fetch XTC and PDB File from my local source. Which...

10 August 2020 5,379 3 View

How to fix error of GROMACS topol.top file?

I am doing MD simulations for protein. When i am running the commands the following error is occurred Command which i have used with ubuntu gmx genion -s ions.tpr -o solv_ions.gro -p topol.top...

27 July 2020 3,199 15 View

Which is the best ELISA assay kit for the measurement of mouse serum and urine creatinine?

Hi, I am looking mouse ELISA kit for the evaluation of creatinine level in serum and urine. Could you please suggest me which kit is most reliable for this assay? Regards, Nirmal

03 December 2019 824 4 View

How to Manufacture the Nano Powder of Zirconium or Zirconia from Micron Size available in market?

Zirconia or Zirconium NaNo Powder Production

26 November 2019 2,247 3 View

Can someone Help me out with a suitable UDF to import variable properties of SUPERCRITICAL Water?

I am not able to hook up my table of ISOBARIC (225 Bar) PROPERTIES OF SUPERCRITICAL WATER (varying wrt Temp) obtained from NIST into ANSYS FLUENT which only accepts a C Code, Piecewise Linear and...

27 October 2019 4,424 5 View

How can I convert charmm parameter and toplogy file in to the amber format?

Hi I am following a paper "Development of CHARMM-Compatible Force-Field Parameters for Cobalamin and Related Cofactors from Quantum Mechanical Calculations". In this paper they used charmm force...

25 September 2019 8,059 7 View

Can the capacitance of a Graphene based FET can be calculate via CV charge discharge method?

As in case of capacitance calculation for super-capacitor the CV charge discharge method is popularly used. Can the similar method be implement to calculate the capacitance for graphene based...

27 August 2019 2,843 5 View

How to I completely drying a solvent casted PLCL film?

I have prepared a thin PLCL film by solvent casting technique. The solvent I used is acetone. I am getting a sticky film even after heating the film at 90DegC for 3-6hrs. Please suggest any...

08 August 2019 6,017 1 View

How to calculate Ligand-active site distance in a ligand-protein complex from MD simulation?

I have run a MD simulation of a ligand-protein complex in GROMACS using CHARMM forcefield. Reviewer has asked me to calculate Ligand-activesite distance and binding free energy of ligand with...

27 February 2021 4,703 1 View

How long does it take to design and validate transition state analogue inhibitors?

Hi, I'm asking from the point of view of designing a research plan: How long (approximately) can it take to determine the transition state structure of an enzyme substrate using kinetic isotope...

14 February 2021 2,610 1 View

How to check if the PMF profile obtained from ABF simulation is correct?

I am doing ABF simulations to calculate ligand binding enegy. The PMF profile that I get using single long ABF simulation is attached as pmf_total.png. When I do this ABF calculation with 10...

10 February 2021 4,170 2 View

Ligands with 3,4,5-trihydroxyphenyl group?

Hi In the design of a bidentate ligand with imine group, is it okay to have a 3,4,5-trihydroxyphenyl group in the structure? In other words, does the 3,4,5-trihydroxyphenyl group compete with...

08 February 2021 4,977 7 View

Is there any difference between "SEP" as a non standard residue and phohophorylated serine?

I am trying to run a molecular dynamics simulation for a ligand that contains a "SEP" residue. also, I am preparing my files using Charmm-GUI using charmm36 ff, but it says that it will rename my...

31 January 2021 6,321 1 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

Best tool to build missing residues, minimize and validate a ligand model?

I am working on a ligand that is co-crystalized to parotein, but the ligand is missing some residues that makes it appear as if it was separated into two ligands! what I need is to connect them...

23 January 2021 3,975 7 View

Can anyone suggest me solution to fix the following problem?

i am working with MD simulations. i am facing error from CGenff server while predicting topology for my ligand file ligand_fix.mol2. error= "readmol2 warning: unrecognized element "Du"readmol2...

21 January 2021 8,290 7 View

Can anyone helps me with Autodock 4.2 scripts error ?

After opening the file, I operate command "Script" --> "Ligand Interactions" --> "Show Ligand Binding Site Atoms" and the warning appears as "This script displays ligands and surrounding...

15 January 2021 5,360 1 View

How to generate topology file for ligand for Gromacs?

Dear all, I converted a PDB file into Mol2 file using Openbabel (H added) and then fixed the bond order number using this command: perl sort_mol2_bonds.pl jz4.mol2 jz4_fix.mol2 When I try to...

22 December 2020 303 4 View