What kind of analysis to perform for protein-ligand interaction by gromac?

More Mahboobeh Eslami's questions See All

How to find out the problem of VMD software when i run it?

Hello I try to install and run the VMD software on windows 10 (64-bit).It doesn`t work and it is closed when I run it. I checked all of tutorials, videos and documents. But they did not work...

22 February 2021 8,211 3 View

How to amplify specific pcr product?

Hello I try to amplify gene of interest by RACE-PCR. For 5` RACE, I saw multiple bands after using specific nested primer. But The desired band was not seen on the gel. What is the reason? When I...

31 October 2020 7,734 6 View

What is the best force field for proteins with folded and disordered regions?

Hello I want to do MD simulation on a protein model to refine its structure. My protein structure have both folded and intrinsically disordered regions. What force field should i choose for this...

23 August 2020 9,381 5 View

How to set up TETRA-ARMS PCR at higher temperatures?

Hello everyone .i'm trying to do TETRA ARMS PCR. My primers have TM :64 and one of the primers has TM :66(Reverse outer). How can I setup at higher temperatures to have mutant band? Because at 65...

03 August 2020 4,742 2 View

What is the best force field for protein MD simulation?

Hello I try to do molecular dynamic simulation with GROMACS software and I work on an enzyme in a plant producing a medicinal secondary metabolite. When i was searching to find a appropriate force...

31 July 2020 171 5 View

How to avoid smear from PCR product on agarose gel?

Hello I used high fidelity enzyme in my PCR and I saw smear on agarose gel. I repeated the PCR with different amounts of cDNA. But I did`nt get a sharp band. what should i do to resolve my problem?

29 July 2020 3,483 10 View

Which one is more important in protein homology modeling ?

I try to make a model with MODELLER software and I decide to use multiple template modeling method. Two template structure I choose for my work, have similar Identity percentage (42.54% and...

03 May 2020 1,263 3 View

How can i detect small size PCR product from primer dimer?

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22 December 2019 387 9 View

How do I choose the major compound of Essential oil?

hi everybody, how do I choose the major compound of Essential oil ? is there any special index or scale for determining the major compound ? what method shall I use ? thanks.

06 December 2019 4,133 2 View

Is it possible to estimate the most recent common ancester using o & 1 data? If yes would you please introduce a software?

Dear professors Respectfully, i know that sequences can help us to reveal the most common ancestor in phylogenetic studies. However, in genetic diversity studies using IRAP, SSR, markers etc, i...

13 November 2019 9,305 6 View

How to analyze a particular region of my simulation box in GROMACS?

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03 March 2021 9,989 2 View

Why might my GFP tag be dissociating from my plasmid after transfection?

I have a set of stably transfected cell lines all transfected with plasmids containing GFP tags on the C terminus. During a western blot using anti-GFP antibody, one of my plasmids has dissociated...

01 March 2021 9,310 4 View

Precipitate after adding laemmli buffer to protein solution containing Potassium Acetate?

Hi, I am running a size exclusion chromatography experiment with a buffer containing Potassium Acetate as a salt. I analyse these fractions through SDS-PAGE. After boiling my SEC fractions in...

01 March 2021 2,622 3 View

What is the most suitable server for predicting protein structures in bacteria?

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28 February 2021 4,521 3 View

Do you need the CMV enhancer before the CMV promotor for a proper function of CMV on the gene that follows?

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28 February 2021 7,127 2 View

Are protein samples in SDS compatible with ELISA?

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28 February 2021 7,370 3 View

How can I calculate the rdf of water molecules around 'Na' ions that are closest(adsorbed) to the nanoparticle(solute)?

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28 February 2021 5,650 1 View

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

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27 February 2021 4,703 1 View

How can I assign a velocity along one direction to CO2 molecules in a molecular dynamics simulation using GROMACS?

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26 February 2021 10,014 3 View

How does GROMACS calculate the average structure of proteins?

I want to get a average structure from a pdb file containing multiple models. I used the command below: gmx cluster -f input.pdb -s topol.tpr -cutoff 20 -method gromos -av GROMACS...

25 February 2021 6,314 1 View

Karim Mahnam

hi the best method for calculate binding energy in gromacs is LIE method also you can change your gromacs trajectory to amber trajectory and use the mmpbsa method.

mmpbsa is one of the most powerful method for binding energy caculation

Akhil Kumar

How to convert gromacs trajectory to amber trajectory ??

You can calculate binding free energy via g_mmpbsa module from trajectory.