Can someone recommend a MD force field for phosphorylated cysteine (3-oxoalanine)?

I would like to do classical MDS of a protein containing phosphorylated cysteine (3-oxoalanine) using GROMACS. Which force field should I use?

07 August 2019 7,344 4 View

Why Gromacs mmpbsa shows 'nan' in energy values?

I have performed simulation using gromacs. The protein is of two chains, I am trying to understand the changes in mmpbsa values between the two chains but I get following. What could be possible...

02 March 2019 1,935 3 View

Is it possible to create gromacs ndx file of two chains as a single index file?

I have performed a protein-protein simulation. I wish to see the change in binding between protein chain A & chain B. How to create a index files of chain A & B and do the analysis? Like GROUP 1 :...

02 March 2019 6,250 4 View

Can GROMACS perform molecular dynamics with different pH? If NO, what could be an easiest alternative?

I wish to study the change in interaction of the small molecule with the protein in respective to change in pH. GROMACS focuses most on protonation state and not directly on pH. So how can I...

01 February 2019 3,095 5 View

How to get the nano-particles of different shapes in 3D PDB?

We have identified nano particles of different shapes (eg Ag NPs in rod shape, round, etc.). we wish to have computational study. Is it possible to draw the structures of nano particles or get...

03 April 2018 3,981 0 View

Is it possible to draw the nano particles using software? If yes, what are they?

We have identified nano particles of different shapes (eg Ag NPs in rod shape, round, etc.). we wish to have computational study. Is it possible to draw the structures of nano particles or get...

02 March 2018 7,111 1 View

Could someone suggest a tool to find druglikeness of multiple compounds at a time (.sdf)?

05 June 2017 8,517 0 View

Why many of the drugs in market do not satisfy lipinski rule?

05 June 2017 2,142 5 View

What are the set of parameters and its normal value used in "Quantitative Estimate of Drug-likeness (QED)" predictions?

05 June 2017 7,745 0 View

When considering molecular dynamics simulation, which is more appropriate? A long run dynamics or multiple run dynamics?

03 April 2017 2,597 3 View

Dear all, I was wondering if anyone knows whether MGLtools and Autodock can run on Mac OS?

I have tried to download the 64-bit version of MGLtools however, as many times as I have downloaded and uninstall the programs, an error arises that the app needs to be updated. Thank you.

03 March 2021 5,997 2 View

What is the production process of CaFe ferroalloys?

I looking for ferro calcium production process

03 March 2021 1,755 4 View

I need to image mesoporous silica nanoparticles that are in ~100 nm size and do high resolution TEM to look at mesopores. what grids should I use?

Need to image mesoporous silica nanoparticles using the TEM. Also, need high resolution TEM images to see the mesoporous structure. Kindly suggest what kind of grids to use. Thanks, Shatadru

02 March 2021 1,787 2 View

Do I need to strip the PVDF membrane before staining it with colloidal gold?

Dear Colleagues, After running Western blot on PVDF membrane and detection using ECL, I would like to stain my PVDF with colloidal gold to be able to allign the ECL image with total proteins on...

02 March 2021 7,829 3 View

Can chitosan alone can act as a reducing agent for Cu(0) nanoparticle sythesis?

[Synthesizing Cu nanoparticles without using chemical reductants]

01 March 2021 8,359 1 View

What are the new 2D nanomaterials were used for Silver nanoparticles stabilization?

In the stabilization of AgNPs are vital in current research interest. However, some of the 2D nano-materials like graphene oxide, MoS2, etc... previously used to stabilize it. But still they shown...

01 March 2021 2,207 3 View

What is the state of the drug inside solid lipid nanoparticles (SLNs)?

I am a little confuse with the mechanism of solid lipid nanoparticles (SLNs). The main point of encapsulating drugs into SLNs is because some drugs have low solubility in water. Therefore, SLNs...

01 March 2021 3,703 3 View

How to check the uv-vis absorption of nanoparticle by surface plasmon resonance?

I try to check the uv-vis absorption of Indium nanoparticle. Now I am measuring in solution, can I measure it in the form of a film?

01 March 2021 930 3 View

Distribution of particles in metal matrix?

How would define the "good" and "poor" distribution of particles within the matrix. Is there a quantitative solution to assess the distribution of the particles, which then having denotation of...

28 February 2021 7,397 8 View

1 nm thick MgO thin-film to be deposited on Si wafer using thermal evaporation. What will be the optimum deposition conditions?

Favourable conditions of base pressure, rate of deposition. Also, by which characterisation technique to be used to verify the thickness of the deposited film.

28 February 2021 3,640 3 View