How can I fix the memory error in Auto dock Vina tools?

More Priyanka Nagu's questions See All

I have got 22-25 colonies on my after transforming the ligation in DH5aplha. Should I screen all the colonies?

I have screened 10 colonies out of 22. But neither get insert release nor the PCR amplification for the desired gene. What should I do, should I further screen the colonies?

02 December 2020 3,225 3 View

Which bacteria can grow on 10x PBS buffer?

I have prepared PBS buffer and components for M9 medium and I store it in freeze, I do not use it if it is more than 2 weeks old. From time to time I check the sterility of these solutions and...

04 November 2020 9,427 6 View

Which model can be used to predict on below data?

I want to predict valuation using verbal SAS but there exists a strong nonlinearity between the two variables which makes unfit to use linear regression. Please see the attached scatter plot image...

05 August 2020 1,602 3 View

Which is the best model to predict student marks based on entrance exam result?

Hi, I have a dataset that contains student data that are nested based on different schools where more that one student belongs to a particular school. student_id school_id non_verbal...

29 July 2020 9,825 18 View

One step RT-PCR enzyme optimisation, can anyone help?

Helping others is the way we help help ourselves! In this case literally!! I work at a biotech company called Genaxxon Bioscience GmbH in Germany. We have an amazing one step RT-PCR enzyme which...

13 July 2020 7,395 2 View

Do Acetonitrile type (gradient grade or non gradient grade) affects the HPLC results?

Trying to develop the HILIC-RID method for sugar analyte but getting very different results between two-run of the same sample. Tried 60 minute washing between two-run. The mobile phase is 75:25...

11 June 2020 8,385 3 View

Why Pseudomonas fluorescens ATCC13525 does not grow on acetate?

I am trying to grow Pseudomonas fluorescens ATCC13525 on different carbon source except glucose in M9 medium but i cannot see them growing on acetate. I am not able to find more information about...

20 February 2020 2,469 6 View

Which funding agency in India will grant traveling allowance for international conference in finance ??

I get an opportunity to present my paper in international conference on June 2020. I am research scholar in management (finance department).Kindly let me know which funding agency will grant...

07 January 2020 7,040 1 View

Is raman peak at 515cm-1 normal for silicon wafer with 532 laser and 600 grating?

We installed new grating to your Renishaw inVia Raman microsscope. While routine calibration of the system, we observed the Si raman peak at 515cm-1 for 532 lase 600 grating and 519.9 cm-1 for 532...

02 December 2019 5,582 3 View

Why does my freshly thawed and seeded HeLa cells look different than usual?

I had stored HeLa cells in -80C freezer for over a month. When I thawed and seeded the cells today, I noticed that the cells looked significantly different than usual cells when floating in media....

25 November 2019 4,352 6 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

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

How can I edit suggested publications?

Hi there! I regularly receive suggestion about papers and authors that are totally out of my area. Does anybody know how I can fix this? Thank you!

01 March 2021 9,574 4 View

What is the ideal efficiency for a qPCR?

hello everyone, I need to do standard curves for my qPCR, what is the ideal efficiency range? I tried a primer (Mglu2 receptor) that gave an efficiency of 90.2%. Is it accepted?

28 February 2021 1,254 3 View

How to calculate Ligand-active site distance in a ligand-protein complex from MD simulation?

I have run a MD simulation of a ligand-protein complex in GROMACS using CHARMM forcefield. Reviewer has asked me to calculate Ligand-activesite distance and binding free energy of ligand with...

27 February 2021 4,703 1 View

Can you perform the Murexide test on samples fixed in Formalin?

I have a fixed sample and would like to use the murexide reaction to test for uric acid composition. I no longer have fresh samples

22 February 2021 1,328 1 View

Monte Carlo simulation?

Hi, i am conducting a Monte Carlo simulation for my new distribution but the MSE values are increasing while the sample size increase, does any experience this issue before and what should i do...

22 February 2021 3,680 4 View

How would I use a glycerol fixation to fix whole brain Drosophila tissue?

I need to take IF images with DAPI on a confocal but I need to use a glycerol fixation. Has anyone done this method before, if so how was it done? Thank you.

21 February 2021 3,081 3 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

Is there any general protocol for immunohistology staining?

I have some fixed slides of tissue and need to do some staining, but I am not sure where to start. There are many protocols online. Any suggestions?

17 February 2021 3,062 4 View

Waseem Ahmad Ansari

Hi Priyanka Nagu

First of all you can open ADT

Go->analyze->Docking-> open->.dlg file of selected complex

Go->analyze->Docking-> open-> macromolecule (Take by default)

Go->analyze->Docking-> open->show interaction

and other way

you can open your complex on Discovery studio and see the interaction in 3D and 2D structure

you can open your complex in Pymol and see bond interaction

If you want only 2D structure so you can go also Ligplot