Can anybody describe briefly how to set up a starting structure of PNA for AMBER molecular dynamics simulation?

I want to study PNA using molecular dynamics simulation, can anybody describe briefly how to set up a starting structure of PNA for AMBER molecular dynamics simulation. If any published protocol...

01 January 1970 3,962 1 View

Does anyone have experience with calculating the distance between group of atoms using Ptraj in Amber?

I am trying to calculate distance between Center of mass of two groups of atoms located at two ends of my system using distance command in ptraj for AMBER trajectories. For calculating the...

01 January 1970 9,137 2 View

Problem with xLeap : Segmentation fault (core dumped)

I am trying to remove some residues from a structure in xLeap with the following command: remove p p.1 where p is the name of unit, But after doing this, as I click to the graphical window of...

01 January 1970 6,214 0 View

Any suggestion for the smoother running of VMD?

I am using VMD LINUX_64 OpenGL, CUDA version in my UBUNTU 12.04 64- bit machine. When I load even small structures, say 50K atoms, it becomes slow. The visualization also run with jerks. Earlier...

01 January 1970 202 5 View

While generating the initail topology and coordinate, when it is better to add ions to the DNA, before or after the solvation ?

While generating the initial coordinate and topology files for DNA simulation in water, we add counter ions to neutralize the backbone charge. I use leap (AMBERTOOLS) to solvate and add ions. But...

01 January 1970 4,359 1 View

How might one define molarity convention for DNA ion MD simulation in explicit water?

Dear Researchers, I have a doubt regarding the molarity convention used for MD simulation of DNA. I neutralized the charge of DNA molecule with Na+ ions in a water box. I want to simulate the...

01 January 1970 3,471 4 View

Can someone advise on hydrogen bond calculation in VMD for AMBER DNA Simulation?

I want to do some H bonds analysis for my AMBER DNA simulation. I am not sure about its terminology, as it shows only two H bonds between guanine and cytosine in the detail log file which should...

01 January 1970 9,927 5 View

Why only 10 NN free energy parameter?

I didn't understand how only 10 pair were chosen in the 1997 PNAS paper (A unified view of polymer, dumbbell) by Santalucia. I don't know on what basis these 10 sets have been chosen. The...

01 January 1970 7,097 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

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

Which cell line should we use to perform biological dosimetry experiments?

We are preparing some experiments based on irradiating cells under different conditions in order to evaluate the effects in terms of DNA damage, genetic expression, etc. As our project is...

01 March 2021 3,355 3 View

Calculating volume of DNA required from DNA concentration?

Hi I am a bit confused. They are asking me to find out the volume of DNA required in ul (a total of 30-100 ng for genomic DNA) from the DNA concentration in the nanodrop reading which was 404.8...

26 February 2021 5,029 2 View

Has anyone used the Illumina ITS1 primer sets?

Hi everyone, Illumina provides a list of primers to amplify with high taxonomic coverage the ITS1 region for further fungal sequencing, but I cannot find the exact amount necessary of each...

25 February 2021 6,969 3 View

Errors in DNA sequences?

I am trying to better understand the scope of DNA replication and sequencing errors, e.g. 1. I have seen similar error rates of 10e4 to 10e5 for cell & instrumental DNA replication,...

24 February 2021 4,397 3 View

What might be the reason for obtaining two bands in plant genomic DNA extraction?

I got a thin band and a thick band i guess it would be the genomic DNA and the 260/280 ratio is 3.

21 February 2021 6,523 6 View

I can detect my protein but the encoding DNA sequence has stop codons within. Should I ignore the stop codons?

I constructed a synthetic DNA library (scFv, VH-VL orientation) with a 3' reporter and 8x histag. I cloned and expressed this gene following which I performed an ELISA. The ELISA results suggested...

19 February 2021 7,006 5 View

Is nanotechnology part of materials science? Is it possible to obtain Pico technology and move from hypothesis to application?

Pico-scale This is three orders of magnitude smaller than a nanometer (and thus most nanotechnology) and two orders of magnitude smaller than most chemistry transformations and measurements. Pico...

18 February 2021 4,540 5 View

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17 February 2021 4,217 3 View