SO Cool!

I thought that the work was finally beginning! I had the best day ever at work yesterday.

The morning was quite uneventful. I finished the whole alpha/beta structures thing. Quite interesting. Had lunch with Derek, and he decided that I should start computational chemistry. YAY! So after lunch, we went to Chandra’s office to transfer some Quanta files to his computer. That was the program that had the various protein structures. The one we wanted was P53, attached to another protein. So we put the P53 on one file, the other bit on another file, all the relevant numbers, energies etc etc on different files, and tried transferring it to Derek’s computer. The first time we tried to run it, the whole thing crashed – at least, it looked like it was crashing – and there was this skull and crossbones staring at me on the page. Derek saw my shocked expression, and he goes “Oh yea, one more thing. It almost never works the first time!” It turned out that the Hydrogen in the Histedine residues weren’t specifying which Carbon atom they were pointing towards. So we made it all HisD (pointing towards carbon delta). Then, after running it again, it turned out that there was another Histedine molecule, so we had to do it again. THEN, it turned out that the Quanta on two different computers named the carbon atoms slightly differently. So, we had to change all the deltas to epsilons. We finally got it to work the fifth time. Sounds frustrating, but it was so cool…seriously!

Basically, what (Dr.) Derek does, is this: he takes the protein structures, puts it in a solvent (on the computer) and makes it move by providing energy. Each movement has to be measured and unraveled, one NANOsecond at a time! And each nanosecond takes a day to work out! So imagine how long one SECOND would take. It’s a tedious job...and he loves it.

So we opened those copied files on his computer, and put the P53 along with the other bit in a cube of side 5 Angstrom. So now we had the protein, in its solvent. We did have to add 3 Cl- ions to neutralise the overall negative charge in the protein, but that worked out! The problem? From what I understood, the final file didn’t transfer properly, and the code isn’t working. So now, he and Sandeep have to figure out what’s wrong with the darned thing!

This entire process took till about 6 in the evening. I didn’t realise the time was flying, and since my phone picked yesterday of ALL days to die, ma was panicking. I met Parita at Bugis, and drove home at close to 7. Long day, but the best one so far!

I have to wait a week for the program to run, and give me results. Guess what I get to do till then? Read up on beta structures. Not that it isn’t interesting; it’s just getting a bit monotonous that’s all. Especially since I got all excited about starting the computing yesterday! Oh well, I’ll get down to it eventually…

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PS - Don't ask me how I know, but this is my 50th post! YAY!