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

More Mahboobeh Eslami's questions See All

Why the sequence of my PCR poduct is very clear without any noise, but very short in size?

I faced with a problem, and I think you can help me regarding this issue. I have sent one of my PCR poducts (ITS1-ITS4) to a company in order to sequence it. Indeed, I sent them various PCR...

01 February 2024 2,626 3 View

Why did I observe more than one band in my PCR product?

What is your solution regarding extra bands in ITS molecular markers? I am trying to use ITS1 and ITS4 markers in 15 plant species. Unfortunately, I only received extra bands instead of one after...

28 November 2023 9,305 4 View

Fatal error: Atom type OUrea (residue UREA) not found in atomtype database??

I am running the pdb2gmx command for my protein using Gromos 54a7 force field, but I have this error: Fatal error: Atom type OUrea (residue UREA) not found in atomtype database while this atom...

04 May 2023 156 2 View

Dear professors, would you please let me know in which case it is possible to synonymized taxa?

I have two morphologically similar species that differs molecularly only by 4 bases. Can I synonymmized them? If not, how many base differences can lead to this taxonomic revision? How do I deal...

10 April 2023 3,602 18 View

What is the highest power transferred wirelessly?

Hi All, I was wondering what is the highest power that has been transferred wirelessly in the state-of-the-art research? and what was the furthest distance for it?

11 March 2023 2,735 4 View

Apply post translational modification in pdb file before MD simulation?

I am going to calculate the binding energy between two proteins, which one of them is post translationally modificated. Is there any way to apply this PTM in pdb file before MD simulation?

18 January 2023 3,728 3 View

How to run dyson orbital in gaussian?

Hi, how to run dyson orbital in gaussian? what is the keyword for this Job? I would like an input and an example

14 August 2022 458 0 View

MonteCarlo simulations for light tissue ?

What is simple way of explaining Monte Carlo simulations for light tissue? I read some papers, but still need more simpler way of explaining Monte Carlo for light transport in multi-layered tissue.

11 June 2022 5,052 0 View

Error while calculating binding energy using gmx_mmpbsa?

I am trying to calculate binding energy between two protein using gmx_mmpbsa, but when I am running the last command to calculate binding energy (gmx_MMPBSA -O -i mmpbsa.in -cs md.tpr -ci...

09 June 2022 3,133 6 View

Is it possible to use such RMSD graph for publications?

I ran a simulation for two proteins in a complex, but the RMSD graph show instability after 45 ns. is it possible to represent such RMSD graph in article or use it for analysis?

22 May 2022 6,152 0 View

Gromacs first step of minimization ?

I have face this problem anyone help me how to solve this issue ?which is below Fatal error: There are inconsistent shifts over periodic boundaries in a molecule type consisting of 78 atoms. The...

07 August 2024 2,598 1 View

Why does my protein refolded to beta sheet during thermal denaturation analysis?

Hi! So i attempted to understand a novel protein behavior towards heat application by analyzing its secondary structure change. I subjected the protein to a thermal denaturation analysis using...

06 August 2024 1,989 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 3,589 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

Transfection in HEK293T cells?

Dear All, I am trying to transfect a pCDNA3.1 vector containing my gene of interest. The purpose is to figure out the localization of the protein of interest. I have fused the protein with GFP on...

31 July 2024 9,892 4 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

How to retain the a GFP tagged gene expression in stable cell line?

Hello , I established a stable cell line expressing GFP tagged to a centrosomal gene having G418 drug selection marker. I validated the stable line by IFA and Western blotting, results are fine....

29 July 2024 5,007 0 View

How to restart MD without using checkpint file in GROMACS?

Dear All Gromacs User I would like to restart MD without using checkpint .cpt files? I heard there is a way for acheiveing this. Any input and sugegstions are most welcome. Thanking You Budheswar

29 July 2024 3,084 8 View

What is the relationship between protein structure and N or C terminal tagging choosing?

I want to do 2,3-butanediol dehydrogenase(BDH) enzyme purification to confirm its activity for 2,3-butanediol. Before that, I need to confirm which N or C terminal tagging is better for enzyme...

28 July 2024 366 3 View

Why cannot i find my protein on cell surface after antibiotic selection of expressing plasmid?

I cannot confirm cell surface protein expression by flow cytometry even after transfection and antibiotic selection of cells. Does it take long for proteins to express on the cell surface? the...

28 July 2024 3,178 3 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.