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

How to indicate the degree of litter decomposed by microbes?

Any technique could detect the degree of litter decomposed by microbes? Or any indexes could do this job? I want to split the contribution of microbes during decomposition, so any suggestions...

23 February 2021 1,362 5 View

How to Implement Elastoplasticity in a PCL model in COMSOL Multiphysics?

I am using COMSOL Multiphysics 5.5. I am trying to simulate the tensile test of PCL scaffolds. However, regardless of the strain, I have the elastic region all the time which is not true when it...

23 February 2021 4,050 1 View

Can we use image data in MATLAB Neuro Fuzzy Designer ?

I have remotely sensed data (image) that I want to use in the Neuro-Fuzzy Designer apps of MATLAB. Is it possible to use an image file in the Neuro-Fuzzy Designer app or only numeric data is...

17 February 2021 1,205 5 View

Would bisulfide sequencing result be affected if the tissue is fixed by perfusion?

I am looking into DNA methylation of mice as an aging marker along with other assays and recently I added brain IF to the list of assays. For this, I need to fix the brain by transcardial...

09 February 2021 9,012 3 View

Why E1g mode (Molybdenum disulfide) is undetectable in Raman spectroscopy?

I synthesized 1T/2H hybrid phase MoS2 on a graphite foil surface by hydrothermal method, and then analyzed it by Raman spectroscopy. As a result, three new peaks correspond to the 1T phase were...

04 February 2021 6,580 2 View

Can I use 500ng of DNA for restriction digestion?

The recommended amount of DNA for restriction digestion is 1ug in a 50ul rx I've got around 500-600ng of DNA in a total volume of 35ul. Would I get satisfactory results with this amount of DNA for...

31 January 2021 729 6 View

Difficulties purifying Outer Membrane Vesicles using a Sucrose Density Gradient: Unable to detect any protein after this process?

I'm currently trying to purify Outer Membrane Vesicles (OMVs) following their extraction from the bacteria I'm working with. After the initial extraction the concentration of protein seems good...

27 January 2021 6,852 3 View

Where can I find these two papers?

14 January 2021 1,572 3 View

What form of data analysis should I use for my pilot study?

I am currently conducting my final year dissertation which is looking at the efficacy of common police lineup practices. However, before I launch my study, I have put out a pilot study which is...

08 January 2021 4,376 4 View

Does any one can help me choose a reasonable basis set for intermediate metal ions interactions with guanine (i.e Fe2+, Mn2+, Cu2+ and exc.)?

Hello every body Does any one has any idea to help me choose a reasonable basis set for intermediate metal ions (i.e Fe2+, Mn2+, Cu2+ and exc.) interactions with guanine or other DNA organic...

01 March 2021 6,187 2 View

How to resolve Gaussian error termination " Error termination via Lnk1e in F:\G16W\l103.exe" for TS(QST3)?

When I run the job for TS(QST3) in gaseous phase, it was completed without any error. But when I add water in CPCM model it terminated with an error: Inconsistency: ModMin= 2 Eigenvalue=...

21 February 2021 3,198 2 View

How to calculate the Atomic Polar Tensor using DFT ?

Dear friends, I am a beginner at DFT calculation. I have done a structure optimization using DFT- B3LYP/6-31G*, Nevertheless, I don't know How to calculate the Atomic Polar Tensor (APT) in...

17 February 2021 9,082 3 View

Access to supercomputer resources in India?

Hello everyone, I want to perform some gaussian calculations and want to use Materials studio for my research work. Can anyone guide me how to get access to supercomputer resources in India for...

15 February 2021 8,264 3 View

Why we use feature normalization before using the Gaussian kernel in SVM?

Support vector machine

09 February 2021 6,405 3 View

Does Gaussian 09W software take too long to give a result if we have a large chemical structure ?

DFT - gaussviev - gaussian09W - HOMO - LUMO

08 February 2021 6,012 5 View

How to calculate enthalpy of formation of Polymers taking into account the terminal end groups?

I am trying to find methods for theoretical calculation of enthalpy of formation of Polymers. till now I have found the oligomeric method (Gaussian) which uses the extrapolation of results from...

05 February 2021 9,707 4 View

How to identify when a gaussian program is about terminate normally?

Dear all, I am trying to optimize a bimetallic complex using # opt=tight b3lyp/lanl2dz scf=qc geom=connectivity. The program is running for around 5 days but the size of the .chk remains same...

05 February 2021 8,721 3 View

I have started a gaussian calculations for DFT analysis of phytochemical, it is showing a error 2070?

I am doing optimization of a phytochemical but when i submitted the file for calculations it shows error 2070. Can anyone please tell me what does it mean? and what should i do to solve it. I have...

30 January 2021 7,932 1 View

Does the power law behavior can be approximated with Gaussians?

In epidemiology, earthquakes, tokamak disruptions etc., there is possibility of approximations with the sequence of Gaussians and with the appropriate risks ( see my papers in Journal of Fusion...

26 January 2021 5,411 5 View