Does AMBER or CHARMM force field parameters have coarsed grained side chain parameters?

I need to coarse grain the side chain with a single atom. However, what force field parameters do I have to use. Does AMBER or CHARMM have any parameters and partial charges for coarse-grained...

31 January 2021 7,091 3 View

Where can I read the force field parameters of amino acids and protein ?

I am a beginner in the field of molecular dynamics and biochemistry. I need the parameters such as van der Waal radii, partial charge of each amino acid. How do I read directly the parameters from...

20 January 2021 3,541 3 View

What is the reference for the partial charges values for peptides shown in avagadro?

I built short peptides in Avagadro, using Build--->insert--->peptide. After constructing the short peptides of 4 amino acids(tetrapeptide). Under the drop-down, View--->Atomic...

27 December 2020 778 3 View

How to compute the Backward kinematics ?

I have been reading this paper. https://cnx.org/resources/9c9fe5128dfef772b498990a94c49df16c4f09ee/transformation_derivations.pdf Here, they have computed for forwarding kinematics to compute...

18 October 2020 8,208 3 View

How to plot the following XYZ coordinate file?

I am trying to plot the following points in VMD. It is plotting as points. However, It is not connecting the points from A to B to C to D to E to F to H by a line. How do I do it? If not in VMD,...

15 September 2020 4,282 3 View

What is the difference between TURN, COIL and BRIDGE in Protein structure?

I have been reading the following (open access) journal, In this paper, they have collected data samples from the loop region and categorically classified into TURN, COIL and BRIDGE, 3-10 helix...

10 September 2020 4,033 4 View

What could be the reason where i got some extra small peaks in my sample ?

Hi all, Actually, I have done the experiment where the single crystalline substrate has used to coat a thin film. In that, I have got substrate peaks and also thin-film material peaks also. But...

16 August 2020 6,532 11 View

How to design of PID controller using ANN?

27 March 2020 5,699 3 View

Hi, I would like to sense the Fe(III) in water, therefore how can I overcome the pH interference?

when adding the Fe compound in the water it gets deprotonated and from strong acid. 1.adding base leads to salt formation 2.adding buffer solution leads to Fe concentration change.

11 March 2020 1,785 3 View

What are the useful packages of i-vector/x-vector extraction in python?

Hi all, Recently, I have involved in the speaker language identification using i-vector /x-vector based approach. Kindly share any useful packages links in python to compile this research work....

04 February 2020 1,591 2 View

How to successfully revive cells stored at -80 degree C for a year?

I am working on C6 cells along with other neuronal cell lines. We have preserved the cells in 90%FBS and 10% DMSO solution. We are reviving the cells after a year and cells are either not binding...

18 February 2021 4,499 1 View

What are alternatives for B27+ Supplement in neuronal cell culture?

Hello everybody In our iPSC-derived neuronal culture we use Maturationmedium, supplemented with B27+. As Thermo Fisher run out of stock and can deliver earliest in May, I wanted to ask whether...

16 February 2021 3,348 1 View

RWP1 growing in RPMI medium?

Hello everyone, Has anyone try to culture the normal prostate RWPE-1 cell line in RPMI medium supplemented with foetal bovine serum? There's some articles available but neither describe details...

08 February 2021 6,455 1 View

Can someone help me to improve the MCF-10A growth?

18 January 2021 7,640 3 View

Agmatin determination with LC MSMS?

I would like to determine agmatine (C5H14N4 CAS 306-60-5) with LCMSMS. The samples are sport supplements. The processing should be just dilute and shoot . I have not yet succeeded in achieving a...

29 November 2020 8,356 4 View

In theory, can metabolic diseases, characterized by the lack of production of a protein, be treated (not cured) by supplementing with that protein?

I was reading about metabolic disorders caused by the lack of production of a protein. Can a possible treatment be to supplement the patient with that lacking protein, or would the body degrade it...

19 November 2020 595 2 View

Do you know anyone who might be interested in running oncology related randomized studies concerning vit. D as profilaxex for oncological problems??

There have been a number of studies relating vitamin D deficiency to cancer and relapse in different types of cancers, for instance Hodgkin's lymphoma. Yet it does not have any repercussion for...

09 November 2020 9,211 2 View

Please, help. Should one or two-way ANOVA be used in case of determining the drug effect of the drug against the background of the model operation?

We studied the effect of a biological supplement on biochemical and hematological parameters rabbits with and without model operation. I have 4 group of rabbits (n=8) and 3 time points (before...

15 May 2020 5,846 17 View

How to make E.coli express virulence and resistance genes?

I'm working with some pathogenic E. coli. I want to grow them in a way that they will express their virulence and antibiotic resistances as much as possible Any suggestions? - Media? - Growth...

22 March 2020 8,444 7 View

How to find sample size of a cross sectional survey study with no previous 100 % similar study?

Hii, I am planning to do a cross-sectional survey study to find out supplement prevalence among Sri Lankan university athletes. During the literature survey, I found that similar studies have not...

19 February 2020 5,133 2 View