How cell wall peroperties of l.lactis may change after surface display of a heterogenous antigen?

Hi there! We are applying L.lactis for expression of a heterogeneous antigen using a cell wall anchor subunit. Cloning process has been verified and expression optimization is up now but I'm...

07 August 2019 6,020 2 View

How can I determine the intact bacterial cell in flow cytometry?

Hi guys! I'm working on a whole cell SELEX project of bacteria for developing a diagnostic tool. Most of bacteria are less than 2 micrometer in size that is interfered with many noises . Please...

02 March 2018 8,100 5 View

Why FITC-nucleotide conjugate emission vanish during SELELX process?

Hi there! I'm using FITC-primer conjugate for amplification of DNA library. The florescent tag is necessary for investigation of SELEX proceeding by flow cytometry technique. The problem is...

01 February 2018 1,691 9 View

How can I optimize a sandiwich aptamer-antibody system?

Hi there!! I have design an aptamer-antibody sandwich ELASA system for a whole cell detection test. Can I follow experiment design process like taguchi designs or should I consider Chequerboard...

08 September 2017 8,643 2 View

Am I allowed to run HCD test with Real-time PCR primers?

31 December 2016 3,358 0 View

How can I run PAGE for alkaline peptides?

31 December 2016 4,284 2 View

How can i install DSSP for gromacs on centos6?

Hi everybody I tried to execute dssp for gromacs 4.5.7 by following this instruction: #sudo wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-amd64 -O /usr/local/bin/dssp #sudo chmod...

03 April 2015 4,591 1 View

How long is an appropriate time for structural change investigation by MD?

Hey there! I'm using gromacs software for ligand binding simulation. I want to investigate structural change of protein after complex formation. How long the MD should last to reach the most...

02 March 2015 1,685 8 View

Why the h-bond may vanished during ligand binding simulation?

Hi there! I have performed MD simulation for protein-ligand binding. I used g_hbond command for protein and ligand interaction analysis. I observed that h-bond numbers reached from 4 to 0 after...

01 February 2015 8,191 8 View

Why is there a disparity between c-alpha elements and amino acid content?

Hi every body I was going to calculate RMSF for residues of protein after simulation. I chose c-alpha group which contained 667 elements. My protein has 679 amino acids and 50 of them are Gly. So...

01 February 2015 1,289 9 View

How to analyze a particular region of my simulation box in GROMACS?

Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...

03 March 2021 9,989 2 View

How can I calculate the rdf of water molecules around 'Na' ions that are closest(adsorbed) to the nanoparticle(solute)?

Hi, I want to calculate the radial distribution function for water molecules around the Na+ ions adsorbed on the surface of a spherical nanoparticle using the gromacs trajectory dynamically? For...

28 February 2021 5,650 1 View

How can I assign a velocity along one direction to CO2 molecules in a molecular dynamics simulation using GROMACS?

Dear all, I am trying to perform a MD simulation about the interaction between CO2 and a polymer. I create my model, solvate it and perform the NVT and NPT equilibration. Now I am not able to...

26 February 2021 10,014 3 View

How does GROMACS calculate the average structure of proteins?

I want to get a average structure from a pdb file containing multiple models. I used the command below: gmx cluster -f input.pdb -s topol.tpr -cutoff 20 -method gromos -av GROMACS...

25 February 2021 6,314 1 View

How to identify or create correct list from GROMACS options during analysis of trajectory ?

During topology preparation using pdb2gmx Protein_chain_A and Protein_chain_B were identified. However, when production MD was completed and I proceeded to do analysis, I find this list : Group...

23 February 2021 5,065 8 View

How to construct different filler shape in MD simulations?

Is there any way to construct different initial filler shapes like triangle, square, rectangle, pillar, and tube in any simulation software.

20 February 2021 1,750 1 View

How to include additional force field in GROMACS?

I have a cellulose model system that is best described by the GLYCAM06 force field according to the literature. However, the set of force fields included in the GROMACS package doesn't include the...

20 February 2021 3,309 3 View

Problem in energy minimization using Gromacs?

I have done energy minimization of DNA using Gromacs with tutorial lysozyme in water. The potential energy curve show a steep drop.

18 February 2021 4,822 2 View

RDF calculation of water inside the Carbon nanotubes?

I am trying to calculate the rdf of water molecules present inside the Carbon nanotube. I tried to do the indexing first using gromacs tool gmx selection. But when it comes to calculating rdf, I...

17 February 2021 1,066 3 View

How to obtain parameters to run a simulation for benzene using CHARMM forcefield in GROMACS?

I have been reading this paper Soft Matter, 2017, 13, 1904 and in this paper, they simulate benzene in GROMACS using CHARMM. They mention that they performed simulations of benzene using the...

15 February 2021 5,561 3 View