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Questions tagged [covid-19]

Questions about modeling related to COVID-19.

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11 votes
2 answers

What are the factors to consider before docking 2 proteins?

With no background in biological science, I need help with docking 2 proteins together. This issue is with regards to SARS-CoV-2. The 2 proteins are Spike glycoprotein and membrane protein. What are ...
SaiSmaran S B PES1201701189PES's user avatar
11 votes
1 answer

LAMMPS code that I wrote not behaving as expected. Some issue with the group & region commands

I am actually working on SARS-CoV-2 proteins. Specifically I am trying to tribologically disengage the Spike Glycoprotein from the Membrane protein using LAMMPS. The method is to use amorphous carbon ...
SaiSmaran S B PES1201701189PES's user avatar
7 votes
1 answer

Which non-commercial software can be used to dock two proteins?

I need to dock 2 proteins involved in SARS-CoV-2. They are the spike glycoprotein & membrane protein. I need them to be docked as described in the image below. Since there are many docking ...
SaiSmaran S B PES1201701189PES's user avatar
6 votes
1 answer

Why am I losing bonds when I use PACKMOL on two proteins?

I recently started using PACKMOL to pack a few proteins together. I wrote this PACKMOL code: ...
SaiSmaran S B PES1201701189PES's user avatar