Can someone help me get rid of warnings when I run Autogrid4 from terminal?

More Sandip Dolui's questions See All

Can your Imagination will Imagine? What you think about real future World in various sectors because of digital & wireless innovations? What are SWOT?

Can your Imagination will Imagine? What you think about the real future World in various sectors because of digital and wireless innovations? How it will change the World? What will be the...

21 December 2020 3,506 7 View

Can Antibody-NHS activated resin complex withstand 1% SDS solution?

I have generated a customized NHS-activated column which is coupled to a particular antibody. As per the manufacturer's protocol (Pierce, Thermo Scientific) I was isolating native protein in...

04 October 2020 8,236 3 View

Why second stage juveniles are used for DNA extraction from nematode for identification purpose? Can I use female or male for the same purpose?

I am working on rice root knot nematode. For identification purpose mostly second stage juveniles are used. I wonder why females or males are not used commonly for the same purpose? I am using...

26 March 2020 7,419 3 View

What is your opinion about patents filed by Academic Institutes/ Universities ?

04 January 2020 9,884 3 View

Glucose-6-phosphate and glucose-2-phosphate metabolism in bacteria when used as an exogenous carbon source?

Can expert inform the metabolic pathway when we feed exogeneous glucose-6-phosphate as a carbon source to bacteria (aerobic cultivation). Also requesting the metabolic pathway when exogenously...

18 August 2019 4,581 4 View

What you do for increasing student's interest and attendance in class?

15 August 2019 133 10 View

How to increase the utilization of renewable energy? What are the barriers for utilization of renewable energy sources?

There are many possible applications and reasons of utilization of renewable energy. Please share your opinion where and how renewable energy utilization can be increased? Also, share your...

03 August 2019 8,105 15 View

Which energy source you prefer for cooking, considering sustainable future? And why?

Which energy source you prefer for cooking, considering sustainable future? And why? Electricity, Solar Energy, Wind Energy, Biomass Energy, Gas/Propane/Heating Oil, kerosene, methanol, ethanol...

31 July 2019 5,000 32 View

How to create research interest in engineering graduate students?

23 December 2018 6,281 3 View

Is there any microorganism who uses carbon monoxide for their metabolic activities ??

I want to work on that microbe but I didn't get it

21 December 2018 5,297 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 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

Do you have any experience with transfection of EBV immortalized B cells with Lipofectamine?

I know that efficiency of transfection for primary B cells is very low with Lipofectamine. But I did not try that for EBV immortalized B cells. Do you have any experience with transfection of EBV...

05 February 2021 4,159 1 View

How do you get around this AutoDock Vina error?

I get the following error messages after running the simulation: Sorry, there are no Gasteiger parameters available for atom ligandx.ligand:A:lig1:O7 AutoDock Vina ligand docking initiated for...

26 January 2021 3,822 3 View

How to generate .dlg files on PyRx?

Hi. I'm using the PyRx version 0.8 and getting the error message: WARNING: Filename mismatch: "2DFN_ADP_CL.maps.fld" :: "..\2DFN_ADP_CL.maps.fld" C:\Program Files (x86)\The Scripps Research...

17 January 2021 843 3 View

Is there any online webserver for DNA-ligand docking?

I have used Autodock 4.2 for docking studies and trying haddock for DNA-Ligand docking. It shows an error and not supported DNA PDB file. Suggest a template for DNA and ligand PDB file and also...

29 December 2020 1,322 8 View

Autodock Raccoon - the following maps are missing?

I've generated a set of maps for my receptor using ADT (AutoDockTools). It has resulted in the files: .A.map .C.map .HD.map .N.map .NA.map .OA.map .SA.map .d.map .e.map But when I try loading the...

20 December 2020 7,721 2 View

How to specify binding sites in AutoDock Raccoon?

Hi all, There are two big questions here. I am extremely grateful for even the smallest contribution that yields a result. This is concerning Raccoon(1) original, not Raccoon2. The original...

17 December 2020 4,302 2 View

How to run AutoDockTool's Autogrid4 command?

Hi all, Please imagine this to be a brand new machine with the latest installation of: Autodock Vina Autodock AutodockTools (MGLTools). I'm following a Nature Protocol for the prediction of...

14 December 2020 2,191 3 View

How to run Autodock 4 , using CONDA environment on server ?

#autodock #virtualscreening Question1: Am I doing this right , means do setting up conda on server works for virtual screening (AUTODOCK)? Question2: How can I modify the script (submit4.py)...

06 December 2020 2,424 3 View

Uttam Pal

There are duplicate atoms in the protein pdb file.

Amneh Shtaiwi

Try to fix the problem >>check the No of H-bonding atom with the given serial No. you can use software's to check the atoms No or u can delete all hydrogen atoms again and added them again by Autodock tools

Mahendra Kumar Mishra

i am facing same problem can any one help me please

Sandip Dolui

Try to remove duplicate atoms from a protein pdb file.

how can I remove duplicate atoms I am just started docking so I have no idea how to perform.

there is one thing more how can I identify the duplicate atoms?