How to perform molecular dynamics simulation of Protein-RNA complex at different pH condition??

04 May 2017 8,319 4 View

How do I perform protein-ligand simulation in gromacs with gold atoms?

I want to run protein-Ligand simulation where gold atoms are ligand. Gromacs is showing error for that. I tried to use Prodrug server also, but it is not generating coordinates for gold...

10 November 2015 4,290 7 View

How can I build the virion capsid from single coat protein?

I am having the full-length homotrimer coat protein's predicted model. I want to rebuild virion capsid (Icosahedral virion) by using this homotrimer. Capsid structure of this virion is available...

10 November 2015 9,219 3 View

Is there any kind of change in pH of cell while it is dying due to viral infection?

31 December 2014 4,222 11 View

How can we calculate the volume of a particular domain in simulation trajectory in gromacs?

I want to check the agonist and antagonist effect of ligands on the same protein by doing simulation studies. Protein functioning is a result of conformational changes in protein structure and...

07 August 2014 5,573 4 View

What is the relation between stability of protein and Gibbs free energy?

If conformational changes are occurring in protein structure then how will it effect Gibbs free energy of that particular protein?

10 November 2013 8,543 14 View

How to predict protein structure along with dsRNA?

I want to model one protein structure along with Double strand RNA molecule. I tried to dock this RNA in protein with the help of HADDOCK server but it is not giving the exact pose which I needed...

07 August 2013 1,636 4 View

How do I infer energy landscape in Dihedral Principle Component analysis in Gromacs?

I am performing MDS to find out conformational changes in protein structure. To verify that result, I have done Dihedral Principle Component analysis (DPCA). I got the result up to energy...

06 July 2013 4,457 0 View

How to do multi-chain and multi-template modeling at same time in modeller?

I want to do multi-chain modeling by using more than one template at one time. How should I do this? Do I need to change model_multiple python script or to change model_multichain script?

05 June 2013 8,949 2 View

I am facing some problems while running a pH dependent simulation of homotrimer. Can anyone help me to solve the given error below?

Fatal error: There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry.

05 June 2013 2,554 4 View

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

Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...

03 March 2021 9,989 2 View

Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence?

I am on the lookout for the Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence. Does anyone know where I can find it? Thank you in advance

03 March 2021 3,568 1 View

Do I need to strip the PVDF membrane before staining it with colloidal gold?

Dear Colleagues, After running Western blot on PVDF membrane and detection using ECL, I would like to stain my PVDF with colloidal gold to be able to allign the ECL image with total proteins on...

02 March 2021 7,829 3 View

Why almost every element would be metallized in sufficiently high pressure and low temperature?

(This statement is from wikipedia, BTW). What is so special about metallic bond that is limiting high-P low-T state of a matter (as long as individual atoms exist, not white dwarf of neutron star...

02 March 2021 3,309 2 View

Do anyone here can help us in the field of molecular docking?

We have synthesized various metal complexes with different environment around the metals. Now to see the application of synthesized complexes we need this study also. we are also interested in...

01 March 2021 1,899 2 View

Why there are two peaks while using the mie plot of Silver nanoparticle?

Hi, I am trying to learn the theoretical modelling of silver nanoparticle using the Mie scattering theory. After that, I discovered a software named Mieplot developed by Philip Laven, where it...

25 February 2021 7,493 6 View

What's the concentration recommend for recombinant protein use in western blotting?

I'm currently working having problem with the concentration for recombinant protein use in western blot, the one been used is Recombinant Human CD19 Fc Chimera Protein-rndsystem which does not...

24 February 2021 8,514 3 View

How to formulate Energy minimization in Molecular dynamics simulation for alloys using meam potential?

during MD simulation, the atoms are not moving as per required. The problem (as per my observation) lies in energy minimization technique. upon application of tensile strain in x or y direction,...

22 February 2021 380 5 View

Magnetismic Gravity in the universe?

MAGNETISMIC GRAVITY What is magnetism? Something magnetic has a + and - charge. If 2 + or - are pushed if + and - are pulled. But what is the main reason for this? Why does magnetism have a pull...

21 February 2021 9,538 3 View

Has anyone succeeded in capturing uranium atoms in a fullerene structure?

Additional questions are: What are the encapsulating atoms? How difficult was the process and what rates were achieved? What factors most seriously affect the economics?

20 February 2021 3,134 5 View