How to use my old Config file in for VS using vina in Pyrx?

Jonathan T Bvunzawabaya @Jonathan-T-Bvunzawabaya

28 June 2021 1 1K Report

Hi guys, iam screening around 1000 compounds in batches using Pyrx. I wanted to know is it possible to in pyrx to load your original grid configuration without manual moving the grid box. Im docking several batches of compounds using the same grid configuration. Please assist, thank you

Xabier Arias-Moreno

Hey Jonathan T Bvunzawabaya did you find out if it's possible to add the configure.txt file on PyRx?

Badges
Science topic

More Jonathan T Bvunzawabaya's questions See All

No title

Hi, I have several doubts about one paper (Systematic Literature Review) that was rejected. The main topic is Single-Board Computers in engineering education during the period 2010-2020. The...

01 March 2021 9,015 3 View

How to find the right number of integration points in second order 3d finite elements?

I am familiar with finite element simulations and numerical schemes like the Gauss Legendre quadrature. I also know that the Gauss integration yields exact values for polynomials up to degree 2n-1...

27 February 2021 6,818 3 View

How to interpolate from a time-series database ?

Hi, I am having trouble with a problem, in the field of Optimal Control and the generation of optimal time-series. Let's consider a system, whose dynamics are represented by dx/dt =...

24 February 2021 9,105 2 View

Must a control group to be in the same semester that a experimental group for a study in education?

Hi everyone, I'm researching about mobile learning in higher education. Due to the small number of the students in the semesters, I cannot have a experimental and control group together. I'm...

22 February 2021 3,653 11 View

What is the best way to isolate Hydrolysable tannins on Sephadex column?

I am currently preparing to isolate polyphenolics (Hydrolysable tannins) from aqueous extract of a plant. I want to set up a small sephadex column to guide the major isolation on a laerge...

18 February 2021 1,455 3 View

Are international conferences a dying species?

In our discipline (chemistry), annual meetings of the American Chemical Society (ACS) used to be mega-events with up to 20,000 participants. The current one will be virtual, and the organizers...

06 January 2021 1,882 5 View

How to avoid rejection of your research paper?

Despite certain disadvantages, peer-review is generally accepted as a quality control of manuscripts submitted to scientific journals. The higher the rank of the journal, the more often...

03 December 2020 3,235 17 View

How important are citations? Are they overrated?

Citations of research papers are the topic of various threads on this platform. Quite often researchers ask how to increase the number of citations. I did my first 30 years of chemical research in...

01 December 2020 6,173 94 View

How to find the number cells in each LSTM hidden layer from python code?

LSTM has two hidden layers, I want to know the number of cells in each hidden layer.

30 November 2020 3,481 4 View

How can we sell chemistry to the public?

Chemistry is frequently termed the "central science". It underlies the foundation of modern civilization (drugs, plastics, textiles, dyes, fertilizers etc.), but the public perception of chemistry...

30 November 2020 1,113 15 View

How to analyze a particular region of my simulation box in GROMACS?

Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...

03 March 2021 9,989 2 View

What is your perception on using visual analysis or quantitative approaches to evaluate data from single-case research designs (n of 1 trials)?

Results of single-case research designs (i.e., n-of-1 trials) are often evaluated by visually inspecting the time-series graph and computing quantitative indices. A question our research team is...

03 March 2021 687 1 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

High aspect ratio hexahedral mesh optimization solver?

I am interested in evaluating mesh optimization solvers that converge to high aspect ratio unstructured hexahedral grids. In other words, I am interested in a solver that optimizes warpage,...

26 February 2021 7,279 2 View

How to approach CFD simulation results of a flow past a cylinder?

Hi all, I'm doing a transient simulation of flow past a rectangular cylinder close to the free surface. As far as I'm concerned, the common practice is to discard the initial stages of the...

25 February 2021 1,348 3 View

How to clean up TEM grid with plasma cleaner?

I need to clean the hydrocarbon contamination on the carbon substrate of TEM grid. However, I heard that substrate could be broken by the powerful plasma. My substrate is pure carbon, with ~3nm,...

23 February 2021 3,262 5 View

Best excel chart to compare algorithms' running time?

Hi I want to compare the running time of robotic path planning algorithms. The grid size is 8X8. I have 100 scenarios of start and goal positions.. Each scenario is run in three obstacles ratio...

22 February 2021 621 1 View

Build an orthogonal box in ASE?

Hello, I was wondering the best way to build an orthogonal box filled with a defined crystal structure in ASE. I know it could be easily done in LAMMPS, but I guess it is also doable in ASE. The...

21 February 2021 5,899 4 View

What are the potential shell well and atomic solvation parameters for the boron atom?

I have a protein-ligand docking project. The ligand contains boron atoms that are not detected by Autodock software. To solve this problem, it is necessary to introduce the boron atom to...

19 February 2021 1,236 1 View

How to visualize stress in a coating defined by "Skin" in Abaqus?

Hello All! I'm trying to model a contact between a coated substrate and a tip in Abaqus. The coating is ultra-thin compared to the geometry of the substrate. So I defined the coating using the...

16 February 2021 1,594 3 View