QuantumATK Forum

QuantumATK => General Questions and Answers => Topic started by: asma on March 10, 2020, 11:46

Title: Virus detection
Post by: asma on March 10, 2020, 11:46

My plan is to build a field effect transistor using quantumwise software to detect viruses such as (HIV-influenza A). Does quantumwise database provide me with the required atoms or molecules to build the virus?


Thanks
Asma

Title: Re: Virus detection
Post by: NW on March 13, 2020, 17:24

Hi,

I converted the HIV virus *.cif file that I got from: https://www.rcsb.org/3d-view/4XFZ to *.py file.

You can download it here and then import it into VNL.

Since I am not expert at HIV virus, please check the link and structure before doing your simulations.

 

Title: Re: Virus detection
Post by: asma on March 16, 2020, 06:59

Many Thanks

Title: Re: Virus detection
Post by: asma on March 29, 2020, 09:57

I would like to ask how did you convert .cif file to python file.
I'm trying with other types of viruses but I'm not getting it right.

Thanks

Title: Re: Virus detection
Post by: Petr Khomyakov on March 30, 2020, 13:02

Having an example cif file posted would be helpful. In general, converting might be tricky, as not everybody sticking to conventions when creating those.

Title: Re: Virus detection
Post by: asma on April 1, 2020, 12:17

Thanks for your reply.
I want to get the python script for the rotavirus displayed in the following link:
http://www.rcsb.org/3d-view/4V7Q
 
I was able to download the cif file but I couldn't convert it to python.
Please advise how to convert it?

Title: Re: Virus detection
Post by: Petr Khomyakov on April 1, 2020, 21:52

The cif-file is 606Mb. Do you really want to model a structure with millions of atoms?

Title: Re: Virus detection
Post by: asma on April 2, 2020, 07:32

I didn't realize that it has millions of atoms.
The truth is that I'm still in the first step (proposal) in this research idea. I want to make sure that I'll be able to design the virus using quantumwise and that the simulation time for each run  will be reasonable. I'm using high performance computer.
Below is another link for a much smaller file:
http://www.rcsb.org/structure/3MIW

Can you provide me with link, tutorial, or explanation to convert cif file to python.

Thanks

Title: Re: Virus detection
Post by: Petr Khomyakov on April 2, 2020, 14:56

In general, if you have a cif-file in your project folder, it should then appear in the QuantumATK NanoLab GUI. After selecting this cif-file in the GUI, a configuration object appear on the LabFloor. This object can then be drag-and-dropped on the text Editor available in the GUI and the corresponding file can be saved as a python file. See also this https://docs.quantumatk.com/tutorials/quantumatk_io_import/quantumatk_io_import.html for other options.

Title: Re: Virus detection
Post by: NW on April 13, 2020, 14:08

Dear asma,

You are right. Sometimes it is not possible to import cif file directly in VNL. I used Material studio software as a bridge. First I imported cif file in Material studio then I converted it to xyz/mol file. Finally I imported the xyz/mol file into VNL.

Hope it works for you as well.

Title: Re: Virus detection
Post by: Anders Blom on April 21, 2020, 02:08

Just a note, the file format used at this website is not strictly CIF, it uses some special conventions to allow it to represent molecules. For instance, there is no unit cell specified (this is actually the error message you get when importing) and it uses Cartesian coordinates which is non-standard. In general this kind of files seem tricky, I tried to convert the PDB version with OpenBabel, but it failed (I might have made some mistake in the options).