How do you find the melting point of a material using the two-phase method with DFT+MD?

Dear all, How do you find the melting point of a material using the two-phase method with DFT+MD? Thanks, Uthpala

02 September 2019 9,650 6 View

What are the best performing real-time machine learning models for anomaly detection?

Specifically, I want to know real-time machine learning models that are capable of identifying anomalies considering streams of data with multiple features (i.e. multivariate time series). I have...

04 June 2019 9,780 3 View

Why does a peak as water apper in GC-MS spectrum at retention time 21.9 & 22.1 when organic solvent analysis with following condition?

Injector @ 300 celcius Oven 100 (3min) Rate 10 C/min Final 300 (2min)

06 February 2019 3,858 3 View

When calculate the volume of the Alo vera gel should I consider the water amount or Is it ok to add just the volume of Aloe vera gel with 98% water?

I want to make thin films with Banana starch by adding different concentrations of Aloe vera gel 2%,4%,6%. So Aloe vera is having about 98% of water.When I calculate the volume of the Alo vera...

05 February 2019 2,591 2 View

Protein expression of Gal-genes in yeast?

Hi, I was carrying out Galactose induction experiments to determine protein stability. However, one of my wild-type strains expressed only a trace amount of proteins, which was unexpected as...

22 October 2018 6,859 4 View

How does distance between two electrodes affect reaction rate of electrolysis?

Hi, I'm doing a school project and was wondering what the effect of changing the distance of the two electrodes is during electrolysis? Thanks!

27 May 2018 7,128 3 View

How can I measure the intensity (power density) of a laser?

I need to measure the power density of a laser. What is the most appropriate equipment to measure the intensity of a laser beam?

10 April 2018 2,227 3 View

How shall I submit data into NCBI?

I did 16s rRNA sequencing for bacterial species and now I have 16s rRNA sequences of 4 isolated bacterial species. Can I upload that data into NCBI ? Can I get accession numbers for each bacteria?

25 December 2017 7,692 3 View

How to write the concentration of the media by mg/L or mg/l?

I found both forms in research articles. what is the correct way of writing?

02 October 2017 8,411 3 View

How is it possible a point mutation to become homozygous from Forwarding primer while being Heterozygous from the Reverse primer?

03 April 2017 3,135 3 View

How to calculate Ligand-active site distance in a ligand-protein complex from MD simulation?

I have run a MD simulation of a ligand-protein complex in GROMACS using CHARMM forcefield. Reviewer has asked me to calculate Ligand-activesite distance and binding free energy of ligand with...

27 February 2021 4,703 1 View

What are the potential shell well and atomic solvation parameters for the boron atom?

I have a protein-ligand docking project. The ligand contains boron atoms that are not detected by Autodock software. To solve this problem, it is necessary to introduce the boron atom to...

19 February 2021 1,236 1 View

How long does it take to design and validate transition state analogue inhibitors?

Hi, I'm asking from the point of view of designing a research plan: How long (approximately) can it take to determine the transition state structure of an enzyme substrate using kinetic isotope...

14 February 2021 2,610 1 View

How to check if the PMF profile obtained from ABF simulation is correct?

I am doing ABF simulations to calculate ligand binding enegy. The PMF profile that I get using single long ABF simulation is attached as pmf_total.png. When I do this ABF calculation with 10...

10 February 2021 4,170 2 View

Ligands with 3,4,5-trihydroxyphenyl group?

Hi In the design of a bidentate ligand with imine group, is it okay to have a 3,4,5-trihydroxyphenyl group in the structure? In other words, does the 3,4,5-trihydroxyphenyl group compete with...

08 February 2021 4,977 7 View

How to Remove different version of atom from pdb Crystal Structure for Docking Preparation?

I am new to Docking and MD, and currently try to catch on it. I try one of the webserver for docking, but unfortunately not working. it says " Your PDB contains multiple forms of the same residue...

08 February 2021 7,426 3 View

Is there any difference between "SEP" as a non standard residue and phohophorylated serine?

I am trying to run a molecular dynamics simulation for a ligand that contains a "SEP" residue. also, I am preparing my files using Charmm-GUI using charmm36 ff, but it says that it will rename my...

31 January 2021 6,321 1 View

How do you get around this AutoDock Vina error?

I get the following error messages after running the simulation: Sorry, there are no Gasteiger parameters available for atom ligandx.ligand:A:lig1:O7 AutoDock Vina ligand docking initiated for...

26 January 2021 3,822 3 View

The dimensionality of protein and ligand is reduced after docking?

I used autodock to complete the docking between the ligand and the protein. I have a question, why the dimension of the result after docking is much smaller than the dimension of the protein...

24 January 2021 7,363 3 View

Best tool to build missing residues, minimize and validate a ligand model?

I am working on a ligand that is co-crystalized to parotein, but the ligand is missing some residues that makes it appear as if it was separated into two ligands! what I need is to connect them...

23 January 2021 3,975 7 View