Which DNA folded model (zDNA, A DNA, B DNA, C DNA, H DNA, Q DNA etc.) to use for nanotube?

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

What kind of fluid could I use for a pitfall trap that also does not invalidate molecular testing?

Hi, I want to start testing pitfall trap to obtain ants samples, but I need to conduct molecular analysis on those insects. So, what kind of fluid can I use? Ethanol expires too early and I need...

03 March 2021 5,978 5 View

How to repeat an operation on an atom selection for multiple times in PyMol?

Hi, I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol...

02 March 2021 4,569 4 View

Does anyone know HRM channel in a 2 plex QIAGEN Rotor- Gene Q qPCR can be used as a separate channel?

I am going to have 3 different probes in my qPCR work that I am going to do. But I realized that the machine we have in the lab is a Rotor-Gene Q 2plex HRM Platform, saying it has green, yellow,...

01 March 2021 8,544 1 View

In Molecular Dynamics Simulation, how do I make changes to the force field according to my protein?

Hi In Molecular Dynamics Simulation, how do I make changes to the force field according to my protein? I got this error in the add-ion stage: Fatal error "./ amber99sb-ildn-HHH.ff / force...

01 March 2021 8,747 4 View

Ashokan k V, sangli

Most commonly and only b-DNA is used, I think so.

Markus W Germann

That depends on what you are trying to accomplish and what solvent conditions you want to use. If you are in aqueous solvents at moderate ionic strength then B-DNA is the one you want. If you are talking about (GC)n sequences in high salt then use Z DNA. if on the other hand you are talking about solvents containing alcohols (dehydrating) then A DNA can be considered. BTW C DNA is a subtype of B and so is D.

B-dna

M. Eugenio Vazquez

I am curious, as far as I know (this is not my field of expertise) DNA-nanotube complexes are usually prepared with single-stranded DNA, and formed through hydrophobic nanotube-base stacking, am I right?. What is the interaction that mediates dsDNA-nanotube complexes?