Akhil Kumar

6 Questions 17 Answers 0 Followers

Questions related from Akhil Kumar

Can anyone help with molecular dynamics of amyloid fibril?

I am doing MD of amyloid fibril pdb in 2BEG with gromos 56 force filled for 20 ns. When I visualize in pymol in my simulation after 15 ns one or two chain dissociate from the protein and come...

18 February 2014 7,256 3 View

Any advice for the simultaneous simulation of multiple ligands?

I have used blind docking (as binding site is not clear) approach to my target protein and finally I have clustered the poses. We have a ligand bind to 3 probable binding sites and have already...

24 January 2014 882 3 View

Interactions between flavonoids or other ligand and abeta fibril?

Number of ligands are reported which interact with the surface/side of amyloid beta fibril (PDB ID 2BEG). But I am looking for ligand which went inside the amyloid fibril and interacted with the...

12 December 2013 8,790 2 View

Retrieval of specific metal binding protein sequence?

I want specific cadmium binding protein sequence and then MSA, I am not able to retrieve cadmium binding specific protein sequence so I can get motif for cadmium.

23 September 2013 8,528 2 View

Workstation recommendations.

I want to buy a workstation for bio molecules simulation for minimum of 100ns. Can any one suggest the best configuration? xenon E5 1650, 3.02 Ghz,12 Mb cache, 12 GB of Sata RAM, DDR3, NVIDA...

15 April 2013 6,539 7 View

Pulling chain B from protein Dimer through gromacs using Justin Lemkul tutorial

We are trying to study the effect mutation on protein dimerization. So we are pulling chain B from chain A of a protein dimer with a pulling force of 0.01, spring constant of 1000 and restrained...

01 January 1970 3,494 7 View