How to create a coarse grained model of a protein and ethanol using martini forcefield ?

I want to create a coarse grained model of a protein solvated in ethanol box. I could do that with water by using charm-GUI and VMD but with non standard solvent it seems complicated. any suggestions?

01 February 2020 1,517 2 View

How to use polarizable force fileds like Drude in NAMD ?

As stated in NAMD tutorial it is presently beyond the capability of the Psfgen tool to generate the PSF file needed to perform a simulation using the Drude model. So how can we generate suitable...

05 June 2019 6,456 1 View

In NAMD, should the flexible cell option turned on during NPT simulation ?

04 May 2019 8,687 5 View

How can I calculate the torsion angles of a specific residue side chain over MD trajectory in VMD?

I performed a 100 ns MD of a protein in an organic solvent and I want to calculate the change in torsion angles of a specific residue side chain over the simulation. is there any script to do that ?

06 July 2018 1,572 1 View

Namd OR Gromacs?

I have been using NAMD for one year now and I haven't used GROMACS yet. For those who used both of them, which one is more efficient?

04 May 2018 9,148 2 View

How can an organic solvent improve an enzyme activity ?

It has been known that most of the organic solvents have a detrimental effects on enzymes activity and structure but, if incubation of an enzyme in a specific organic solvent lead to an increase...

02 March 2018 5,703 6 View

What is the best concentration to study the effect of an organic solvent on enzyme?

I am studying the effect of different organic solvents on lipase stability. To compare the wild-type enzyme with it's mutants in terms of stability, should I work at very drastic conditions like...

02 March 2018 2,325 5 View

How can I run a repetition of MD simulation using NAMD ?

I performed a 50 ns production simulation for a protein in an organic solvents using NAMD. Now I want tp run a repetition for the simulation. I read about different approaches but I confused. can...

01 February 2018 1,881 7 View

Using Bradford assay at very low protein concentration ?

03 April 2016 3,723 6 View

How do large proteins fold?

10 November 2014 1,235 4 View

How to compare two groups with only two measurements?

Hiiiii everyone! I have an enquiry on statistical analysis. I was looking for many forum and it's still cannot solve my problem. I want to compare means of two groups of data but only with two...

03 March 2021 8,796 3 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

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

What's the best way to measure growth rates in House sparrow chicks from day 2 to day 10?

What's the best way to measure growth rates in House sparrow chicks from day 2 to day 10? Since, the growth curve from day 2 to 10 won't be like the "Logistic curve" it might not follow logistic...

03 March 2021 1,401 3 View

Does any one know how i can prepare liver tissue with transmission electron microscope with good fixation?

i have problem in preparation of liver tissue with bad cell organelles and how i can adjust osmolarity

03 March 2021 8,890 1 View

Do we need to write protocol for a second study of a systematic review that has been registered and published?

I have conducted and published a systematic review and meta-analysis research with the topic related to public health and health pomotion (protocol was registed in PROSPERO). Now we want to...

03 March 2021 8,920 3 View

How to increase a model accuracy ?

dear community, my model is based feature extraction from non stationary signals using discrete Wavelet Transform and then using statistical features then machine learning classifiers in order to...

03 March 2021 6,994 5 View

I need to image mesoporous silica nanoparticles that are in ~100 nm size and do high resolution TEM to look at mesopores. what grids should I use?

Need to image mesoporous silica nanoparticles using the TEM. Also, need high resolution TEM images to see the mesoporous structure. Kindly suggest what kind of grids to use. Thanks, Shatadru

02 March 2021 1,787 2 View

Do I need to do linear regression before running mediation analysis using PROCESS MACRO by Hayes ?

I just wanted to check if I need to run a linear regression separately if I am using PROCESS MACRO to run mediation analysis. Thank you.

02 March 2021 4,359 3 View

Sample dilution for quantitative analysis using ELISA?

If the detection range is in ng/ml but the reference range is in ug/ml for a molecule or protein in serum or plasma .how to dilute and what is the initial volume to be taken for quantitative analysis

02 March 2021 7,670 3 View