Which force field parameter file is suitable for TMAO?

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Seeking Advice on Viability and Execution of Undergraduate Thesis Topic?

Hello everyone, I am currently developing a thesis proposal and would appreciate your input on its viability and how to effectively carry it out. My proposed topic is: "Does the perceived threat...

10 August 2024 8,992 0 View

To perform transfection with DharmaFECT Duo in AGS cells. Could you tell me what the ideal concentration is to avoid significant cytotoxicity?

I would like to perform transfection with the reagent DharmaFECT Duo (Horizon) on the AGS cell line. Could you please inform me of the optimal concentration to use without causing cytotoxicity in...

03 August 2024 3,851 1 View

What is meant by baseline of FTIR data?

I got comment on my FTIR data figure from a reviewer. The reviewer said "FTIR data in Figure should be repeated. there is no bassline." I made Y off set comparison graph of FTIR on OriginLab. Can...

03 August 2024 6,070 3 View

What is Random Audit?

HI there, I've came across several articles discuss about random audit an Non random to tax evasion or compliance. Most of the articles is relating about effect of audit (random or non random)...

31 July 2024 5,309 7 View

Is the mentioned CV graph a valid one as this graph have only one peak prominent (reduction)?

I have used Prussian blue nanoparticles as a redox couple. The PBNPs have been made using only one salt precursor. Also, during scan rate studies, a small oxidation peak can be consistently found...

31 July 2024 9,697 0 View

How we can use lattice-based cryptography for construction of S boxes?

Please suggest basic literature on lattice-based cryptography. A kind response from the cryptographic community will be highly appreciated.

24 July 2024 6,291 4 View

I am working on III-V based tandem solar cells.Can anyone explain that solar cells work under forward or reverse biased conditions?

I want to know that n-doped side of solar cell is connected with positive or negative electrode.

20 July 2024 1,348 2 View

Can it is possible to find the cleaved sequence when a protein cleaved by a heamaglutanin protease (HA/P) by any bioinformatics tools?

Bioinformatics tools like peptide cutter

15 July 2024 6,453 1 View

Hello, does anyone know how I can get coordinates of two specific points on a moving body in Abaqus when applying a vdload subroutine?

Hello I am trying to simulate repulsive force of two permanent magnets in Abaqus. I have implemented Force equations into a vdload subroutine. sensitive parameters are the center to center...

15 July 2024 3,491 0 View

FACS markers to characterize rat bone marrow-derived macrophages?

Dear all, I am looking for FACS markers to characterize my rat bone marrow-derived macrophages (M0). They were differentiated from monocytes with M-CSF. I am considering to use CD11b/c and...

15 July 2024 4,615 1 View

How to increase simulation box size?

We intend to study the interaction between peptides and polymer (like PP, PE and PS) through MD simulations using Martini force fields ( Martini 2 for PP and Martini 3 for PE, PS). We have...

08 August 2024 4,842 0 View

I want to remove Urea from my protein sample?

I want to remove Urea from my protein (6kDa) sample. I did use : 1. Step down the Urea gradient (dialysis) in order to remove urea and refold my protein, but my protein still contains urea in the...

06 August 2024 1,350 4 View

Do you think can be any gas and oil reservoirs in central of Iran?

I want to know more about gas and oil reservoirs in Iran.

14 July 2024 3,350 2 View

How to apply virtual site for a polymer?

Dear All, I have a PDB structure for a complex and large polymer. I need to perform MD simulations using the OPLS-AA force field. I obtained the force field parameters from LigParGen and created...

11 July 2024 5,109 0 View

Can I use different force field for protein and ligand?

Hello, Dear! Generally, I used CHARMM36 + cgenff force field for simulaiton. But,, due to certain parts of lignad, force field cannot be generated using Cgenff. Can I use different force field...

10 July 2024 9,513 3 View

I found trouble to run MD of my peptide with PTM in different force field. In Charm-GUI, it cant recognize the engineering residue. What can I do now?

I am working on my PTM project. I have some peptide. I got the result of doing MD of those peptide without PTM in different force field like Charm-GUI, Amber, Gromacs. Now I have to do MD of those...

05 July 2024 9,346 0 View

How validate the dynamic molecualr simulation with experimental data?

I used forcite module of Material Studio software to simulate the dissolution of zinc production waste in deep eutectic solvent. UFF force field has been used for the optimization of molecules,...

02 July 2024 7,494 1 View

Thin DNA gel loading sample tips?

I have a 0.25mM thick gel and I am having trouble cleaning out the wells to ensure constant sample application. I usually use a thin syringe to get into the wells and rinse them out with running...

01 July 2024 2,124 2 View

Which is true nano nitrogen or nano urea?

Some scientists use nano nitrogen and some use nano urea, even though the process used the same for preparation. So, which is true nano nitrogen or nano urea?

28 June 2024 2,885 6 View

I tried to do simulation using YASARA software for an optimized ligand after docking but an error is coming what should I do?

The error message is "Angle parameter for atoms42-45-15 (cf-nu-ns) not found in the force field. Initialization is not possible, check atoms for incorrect bonds, then update the force field's...

27 June 2024 3,446 3 View