Adventures in Computational Chemistry

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COVID projections till July end

This last week seems terrible. The kind of spurt we saw in last many days was unexpected. Yesterday's count was 45000+. I did not expect. Are coming days going to report bigger numbers than this? We need to understand the cycle it follows. Mumbai is a good example. Since beginning Mumbai was heading the race. While other cities were reporting the count in 10's or 100's, Mumbai was reporting in thousands. back then, as much as 60-70% of Mahrashtra's total count was coming from Mumbai. Now after a period of almost 3 months, Mumbai is lagging behind. Pune, Kalyan, Thane have overtaken Mumbai. The famous hotspots of Dharavi, Dadar, Sion, Worli are longer uttered in the news. Of course, the counts are still there, but they do not attract any more attention. This is a cycle which will be followed in every new red zone area. The point is how big spike we allow the zone to get and how quickly we nab it. Delhi at one point started competing with Mumbai/Maharashtra. But, it h

COVID-19 Projections -till 22nd July

How would you call the COVID-19 situation in India for the last week. In contrast to what I hear around, I would say, the situation in India is improving. Lets see the reasons why I feel so: - Recovery rate has gone up to 63%. So, there is almost 2/3rd chance of survival for every person getting infected by COVID - The mortality rate has now reduced down to ~2.5%, way down from 3.2% in a 10 days duration.This is happening because of more and more testing. Today's report said, we did record 3.2 lakh testing in a day. This implies that the possibility of death because of COVID-19 is getting low. It may mean, most of the people around can do fine with a little low panic level. Of course, precautions are necessary, if you don't want to fall in that very low 2.5% mortality set. Coming down to numbers. I am happy to see that India deviated significantly from my mid-July projection of 10.25 lakhs. Good to see the lowered down number. This shows the kind of

Material Studio - selective molecule movement

So, working with Material Studio is awesome. You get to handle bigger, complicated and even unimaginable system. But I am facing problems in very minute functioning. I recently faced two problems, but managed to resolve on my own. Somehow, tutorials doesn't help in resolving them and you end up doing some exercise on your own to get the solution. Among these, the problem of bringing two molecular structures in one window and then adjusting one molecule by moving it around, while other structure remains untouched, as it is. Actually, this should not be a problem to do. There is a simple way of doing this. Select the molecule to be moved and then there is a symbol (button) to select, which allows you to selectively move that molecule only. This is the same way it can be done in Material studio too. But among all the dozens of symbols, the new person handling MS, kind of gets lost. So, what he does is check the tutorials, for any help. But the tutorials don't talk about suc

Viewing Margin ruler in MS Word

I am making a note of this option here, so that next time ( which is like 5-6th time), when I want to have margin ruler in my word file, I will know where to look for it. When ever you have to work on a new computer and on opening word file, if the margins of the page are not set properly, you end looking at the top of the page searching for margin ruler to quickly adjust the page. At times, the new computers settings may not have these rulers visible on the page. This ruler is very important, like if want to change the margin or arrange the spacings of bullets, the margin ruler is the easiest option to use. So, next time, if the margin ruler is missing, follow these instructions. All you have to do is click on view option. Here, you will find a section of Show. In this section, there is an option of Ruler which you have to select. Once selected, the margin ruler will appear on the word page you are working. Its simple act to perform, but difficult to remember.

AutoDock Vina protocol: For Molecular Docking

There are many softwares available for carrying out molecular docking calculations. Many of these softwares are paid, while some of them are free. AutoDock is one such freely available software. Earlier, there was AutoDock 4.0 version available. One of the problem with the software was the space it would occupy, if you attempt to do multi docking. Recently, there is another algorithm made available under autodock. It is called AutoDock Vina. This is more efficient, robust and fast algorithm. There are many tutorials available to learn AutoDock Vina including: http://autodock.scripps.edu/faqs-help/tutorial/using-autodock-4-with-autodocktools/2012_ADTtut.pdf and also a video tutorial http://vina.scripps.edu/tutorial.html But for some reason, few changes or explanation in little detail is always required to make it understandable for a beginner to follow. Here is a protocol designed in our group, which our Master's student follow to get acquainted to Molecular Docking s