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

04 April 2018 0 4K Report

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 them from any databases in .pdb or .mol, etc.?

Badges
Science topic

Similar topics
Chemistry
Nanotechnology
Nano

More Thirumal Kumar's questions See All

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 7,495 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 2,121 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 6,435 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 3,264 5 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 7,266 1 View

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

Can someone suggest free online/offline tool to predict the drugliness of the multiple small compounds in sdf format? I tried DrugLito, but it is predicting incorrect values. So I am looking for...

05 June 2017 8,668 0 View

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

I have gone through the paper entitled "Quantifying the chemical beauty of drugs by Bickerton et al., 2012" but I am unable to understand the normal values for each parameter (MW, LogP, etc.)...

05 June 2017 7,915 0 View

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

When there is a set of parameters for drug-likeness such as MW, LogP, HBD, HBA, etc., why are some commercially available drugs which are known to best don't satisfy it?

05 June 2017 2,333 5 View

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

When I go with Gromacs protein simulations, should I consider about performing long run (at least 100ns) or multiple runs (at least 2 runs)? Which one of these could be more reliable and why?

03 April 2017 2,799 3 View

How to find the average distance moved by metal from the protein using Gromacs?

I used mindist of gromacs to find the distance between the proteins (native and mutants) and the metal (metalloprotein) over the simulation period. I have the output in form of graphs. Is there a...

02 March 2017 680 2 View

Can you suggest reliable sources defining "3D mesh" and "3D city models"?

Dear fellow researchers, I am currently working on a paper where I need to provide a reliable reference that defines and distinguishes between 3D mesh models and 3D city models. Although I am...

06 August 2024 9,986 2 View

Nano Orange protein quant on the Quantus fluorometer?

Is anyone here using the Thermo Fisher Nano Orange kit for protein quantification, and detecting the fluorescent signal on the Promega Quantus? We are struggling to make sense of the standard...

05 August 2024 8,946 3 View

What are the shear and normal stiffness values of an LLDPE liner in 3D numerical modeling of a stockpile?

I am seeking experimental or applicable data for the liner (LLDPE) interface in FLAC3D numerical modeling of a large stockpile. Could you please recommend suitable references? The preferred data...

05 August 2024 3,665 0 View

How to Add Missing Water Molecules in Protein-Membrane Simulations?

I have protein-membrane simulations (PDB, PSF, DCD) and have noticed that water molecules near the protein are not visible in the simulations. How can I fix this issue? Is there a way to place the...

04 August 2024 1,200 2 View

Which distribution type should I use when calculating the average particle size from TEM image? and how to calculate the error ?

average particle size calculation from TEM

04 August 2024 2,921 1 View

Who of all the Global Scientific community will help me Prof. Dr. Yoshida make way for TPEOM, MEC ~EMC to return the atmospheric gases to the norma ?

TEP presentation caption (The Environmental Project) Re: Why should Washington’s DC, or any country government point of location think of as nowadays of as to being 'tomorrow as to come! if it...

03 August 2024 2,484 1 View

How to load and plot 2D-PIV (particle image velocimetry) recorded velocity vector field in Techplot?

Dear Researchers I need to know, how to load and plot 2D-PIV (particle image velocimetry) recorded velocity vector field data in Tecplot? Thank You

02 August 2024 3,615 1 View

Does the delta function actually make sense to use on point particles?

The delta function seems produce logical contradictions when analyzed on a fundamental level. I would be curious if anyone else agrees.

31 July 2024 10,109 3 View

CAD File of human's & rat's respiratory airways ?

Dear all, I am working on particle deposition in human's & rat's respiratory airways using CFD and I am looking for the 3D CAD file for my simulations (STEP or IGES format). If somone has such...

29 July 2024 1,092 2 View

What are the modern methods for detecting nanoparticles?

Some of the techniques I am familiar with are standard. I would like to know which of the two methods under study is preferable, as well as the cost and list of particles and devices needed in...

22 July 2024 1,921 3 View