Could anyone point to force field parameters for phosphorothioate oligonucleotide??

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Could anyone point to molecular mechanics force fields for selenium nanoparticles?

Selenium nanoparticles (SeNPs) have shown vital prospects in cancer medicine and nutritional science. Has anybody tried to create SeNPs from their hexagonal lattice cell and model them using...

11 December 2018 7,309 4 View

How to apply position restraints for carbon nanotubes in GROMACS?

I am running a system with protein and carbon nanotube using GROMACS 5.1.4. I used position restraints for carbon nanotube however, during NPT run (both protein and carbon nanotube fixed),it...

09 October 2017 1,493 3 View

How to perform simulation of carbon nanotube in GROMACS in NPT ensemble?

I have gone through carbon nanotube guide on GROMACS website. http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube I have a nanotube aligned to z-direction. I am trying to simulate...

09 October 2017 4,206 2 View

Does anyone have parameters for carbon nanotube (CNT) in AMBER package format?

There are many papers on MD simulations of proteins with carbon nanotubes using AMBER force field. I was wondering if anybody can provide parameters (frcmod or lib files) for carbon nanotubes in...

07 August 2017 557 1 View

How to calculate number of Nanoparticles given wt/wt %?

I know the size of nanoparticle and number of lipids in system. A 5nm gold nanoparticle has ~4000 atoms. A paper suggest lipids:Au ratio = 0.98 % wt/wt. How can I calculate the number of gold...

06 July 2017 5,680 2 View

How to deal with water bubbles during NVT runs with position restraints in a molecular dynamics simulations??

I have been running protein simulations using explicit water and have been using the stepwise minimization (water first followed by solute) and then heating (NVT) followed by density equilibration...

02 March 2017 1,249 2 View

How to build (replicate) lipid monolayer systems using gromacs?

I have a pdb file of coarse grained lipid monolayer system consisting of 64 DPPC lipids. The pdb file is missing box information. I am interested in simulating nanoparticle penetration in...

01 February 2017 2,732 1 View

Simulating chitosan using Glycam force field?

Is there any publication reporting simulation of chitosan using Glycam06 force field?

11 December 2016 2,121 0 View

What is the stereoisomerism in divalen cross-links found in collagen?

I was wondering if anybody has worked with chemistry of these two cross-linkers and have characterised by FTIR or MS whether they are cis/trans or S/R isomers? Apologies: I am not a synthetic...

08 September 2016 8,660 4 View

Anybody acquainted with simulations of hydroxyapatite surfaces in AMBER?

Dear list, I am trying to simulate protein unfolding on hydroxyapatite surface using AMBER MD package. I got the parameters for HAP (based on the interface force field). I prepared the system...

07 August 2016 6,889 0 View

Is there a problem with my RNA pellet?

Hello, I am currently having problems with RNA extraction. I am using mouse liver (C57BL6J), and I have extracted RNA from mouse liver before. Before this experiment, my final RNA pellets were...

11 August 2024 7,082 3 View

Strugglling with m6A dot blot any suugesstion ?

I have been doing the m6A dot blot for a while with no improvement, I am extracting the RNA, and I can see the dots although the three biological replicas give a different reading on the memberan...

10 August 2024 8,539 5 View

RNA Extraction Using Hot Borate Method No Longer Working?

I've been performing RNA extraction on cotton petiole tissue for a few months now using the method described in the following paper, a derivative of the typical hot borate method...

08 August 2024 9,882 2 View

How to increase simulation box size?

We intend to study the interaction between peptides and polymer (like PP, PE and PS) through MD simulations using Martini force fields ( Martini 2 for PP and Martini 3 for PE, PS). We have...

08 August 2024 4,842 0 View

Does Anyone have expertise in in vitro transcription and RNA pull down assay?

I am currently working on LncRNA; to know the lncRNA-protein interactions I want to do RNA pull down assay, so I need to design primers with T7 promoter. I need assistance in this regard.

07 August 2024 6,622 1 View

E.coli contamination in human RNA seq data ?

Recently, we observed that 99% of the sequences in our RNA-seq data corresponded to the E. coli genome. Despite multiple DNAse treatments after RNA extraction and ribosomal depletion, we were...

06 August 2024 807 3 View

RNA later for the preservation of RNA in fecal samples at room temperature for one day (37°C)?

I am planning to collect human fecal samples for metatranscriptomic analysis using MGI. These samples are from indigenous people living in a region with high temperatures. I will have access to a...

06 August 2024 1,367 3 View

Do you have good tips for seaweed tissue preservation in the field for post RNA extraction?

I will be with my students collecting seaweed samples in a marine farm and later we will process this tissue for RNA isolation and further sequencing. Does anyone have tips on how to collect the...

04 August 2024 501 2 View

What is the acceptable p-value cutoff for GO enrichment analysis ?

I have an RNA-seq data that I have analysed using Limma-voom and have extracted the gene IDs, log2FC and the p-values. At p value < 0.05, I have over 10,000 DEGs, however, when I run the GO...

31 July 2024 225 2 View

Inquiry on Maximum Nucleic Acid Volume for 2.5 mL Liposome Solution?

I am currently working on a project involving liposomes and need to determine the maximum volume of siRNA that can be added to a 2.5 mL liposome solution with a total lipid concentration of 10...

30 July 2024 6,420 1 View