Has anyone tried the new AMOEBA force field for nucleic acids (Zhang et al, 2018) on protein-DNA or protein-RNA simulations? I'm curious to see how the torsion parameters manifest in simulating protein.
I think AMOEBA only alters the charge-charge interaction via multiple expansion and does not touch the torsion.
I'm involved in a study of odor control technologies for municipal wastewater treatment plant. One of the control options involves a chemical 2-stage (acid/alkaline) packed bed scrubber. The...
03 March 2021 3,661 2 View
I am try to make the Paal Knorr reaction between 2.5 hexnedione and 6-amino hexanoic acid, my problem is type of solvent to use, because 6-hexaminohexanoic acid is soluble in water but I am not...
02 March 2021 4,443 2 View
Hi all, I need to cleave the ester in Ethyl 2-amino-1H-imidazole-5-carboxylate to make the carboxylic acid and retrieve the product from solution to use in downstream applications of linking to...
01 March 2021 8,766 3 View
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
I am doing a acid and a chiral amino alcohol reaction using DCC and HOBT in DCM or THF? Can anyone suggest me how to remove DCU and HOBT from a reaction mixture??
28 February 2021 2,153 1 View
28 February 2021 5,433 3 View
hi everyone, I'm interested in the field of vaccine design specifically multi-epitope cancer vaccines , I want to know if there is a minimum and maximum number of epitopes we could use in a...
27 February 2021 3,882 3 View
I am working with Polyacrylic acid (100.000Da) and instead of water, I need to use another solvent (dioxane) to dissolve PAA. However, because of the high molecular weight, it's quite hard to...
25 February 2021 2,225 5 View
The limit test I'm referring to is USP method II. In this procedure you need to dropwise add 6N of NH4OH to the sample until it the pH is alkali. After that you need to dilute and add HOAc until...
23 February 2021 2,049 3 View
To do liquid biopsy and look for specific gene expressions there are so many published papers. Thera are different protocols and procedures used to isolate circulating cell free RNA or mRNA from...
23 February 2021 7,326 5 View