Suggestions for charge calculation (delocalized)?

I have modeled an oxocarbenium ion like transition state (at B3LYP/6-31+G* level of theory) with overall charge of -1. I would like to calculate and check partial charges for the molecule. So far...

05 June 2018 475 3 View

How to plot a reaction profile?

I have obtained zpe corrected energies for reactant, TS and product states. I can plot a general scattered plot using MS Excel (but not that great). I would like to know how to plot a reaction...

05 June 2018 9,032 3 View

Molecular docking/MD simulation to analyze TS stabilization?

I was able to successfully locate and confirm TS for my glycoside hydrolysis reaction. As the next step i thought performing molecular docking followed by SMD QM/MM calculation. In doing so i...

04 May 2018 2,863 5 View

How can I use spartan out files instead of gout in Amber 16?

I have been using Amber16 MD suite. As far as I have come a across respgen program in the suite only supports Gaussian output file as the preliminary input. Due to the fact that I follow Spartan...

09 October 2017 4,161 1 View

What is multiple ligand docking approach?

Can someone please elaborate me on the idea of multiple ligand docking approach and how it is done? What really can be predicted using this approch? Thank you.

01 February 2017 1,303 1 View

Simulated annealing in PyRx time consuming?

I have used LGA and found the results very much promising. Currently i am into simulated annealing with only 100 small molecules and found it has not moved forward even after running for a day. Is...

08 September 2016 4,351 2 View

How to perform QM Reaction study on Enzyme Inhibition?

For MD Simulated protein-ligand complex I have extracted the ligand and the reacting residues(as mentioned in literature) for further kinetic study. I have imported this model to spartan software...

01 January 1970 9,047 7 View

What is the best way to analyze binding energy for a small molecule docked in to several snapshots?

I have run vina for 6 snapshots of pre equilibrated cystal structures with several ligands. Now I have 6 vina energies per small molecule. What is the best way to analyze and filter results? I...

01 January 1970 3,416 4 View

Why does blocking with my immunogenic peptide cause nuclear fluorescence in ICC?

Hi all, I am validating a polyclonal antibody raised against human ANT4, through WB and ICC. In most of my controls, the antibody shows very little off-target binding, but when I pre-incubate the...

03 March 2021 5,999 3 View

Have someone successfully used the ER alpha (Santa Cruz sc-8002) antibody in immunostaining ?

Santa Cruz now recommends this new antibody (F-10) but I can't find a publication using this reference. I'm working on human et non human primate hypothalamus and so far, it doesn't work. Is...

02 March 2021 10,003 2 View

Does Napabucasin soluble in dichloromethane and in ethanol?

I need to prepare a solution of Napabucasin (inhibitor of cancer cell stemness) in dichloromethane. The drug is expensive, so maybe somebody already tried to do it. If it is soluble, what is the...

02 March 2021 9,945 3 View

Help request in CST microwave?

im working now on TPV solar cells and metamaterials and i realy need our help in CST microwave i have a tpv cell simulation and i want to extract particullarly the absorbtion of only the active...

02 March 2021 2,246 2 View

Energy minimization in LAMMPS using NVT ?

How do I do energy minimization in lammps with NVT ensemble ? I am using the following command and it does not seem to work. It stops at extremely high energy and gives me the error zero search...

01 March 2021 2,294 3 View

Could you please recommend some good journal that accept very long revie papers (approximately 6000+ words) in neurosurgery, cancer biology ?

Could you please recommend some good journal that accept very long revie papers (approximately 6000+ words) in neurosurgery, cancer biology ?

01 March 2021 8,087 3 View

Which cell line should we use to perform biological dosimetry experiments?

We are preparing some experiments based on irradiating cells under different conditions in order to evaluate the effects in terms of DNA damage, genetic expression, etc. As our project is...

01 March 2021 3,355 3 View

Precipitate after adding laemmli buffer to protein solution containing Potassium Acetate?

Hi, I am running a size exclusion chromatography experiment with a buffer containing Potassium Acetate as a salt. I analyse these fractions through SDS-PAGE. After boiling my SEC fractions in...

01 March 2021 2,622 3 View

Is CD44 degraded in lysosome together with hyaluronan after CD44 mediated endocytosis of hyaluronic acid?

Also when RHAMM binds hyaluronic acid, they get internalized, will RHAMM also be degraded? Or both CD44 and RHAMM will be transferred back to the cell membrane? Asking for breast cancer cell line...

01 March 2021 8,169 2 View

Dapi fluorescence protocol for colon cell lines ?

28 February 2021 2,534 2 View