The Art of FREE Molecular Docking (Using DOCK 6.1) (Part 2)

Step by step docking

In this article, I am only going to SUPPLEMENT the tutorial provided at the DOCK website. Mainly the things which I found troublesome for me. So you should check out the tutorial first for a better understanding on the steps.

The steps in docking using DOCK are:

1) Structure preparation (enzyme and substrate)
For structure preparation, we will have to modify the 3D protein pdb file we have. I used a modeling program called Chimera (as what the tutorial advised), which is available free of charge from the Chimera website (http://www.cgl.ucsf.edu/chimera/). Structure preparation was a straight forward process. I mean, you only have to follow the tutorial to do so (it's already quite clear).

Just remember to prepare the charged mol2 structure of the ligand bound to the pdb protein's active site. You will need it if you want to be more efficient in the grid and sphere generating process. Even though you are not going to dock the ligand. I didn't identify this from the beginning, which created a problem in the sphgen - sphere generating procedure (it took too long, it could take for about 8 hours on my 1.6 Ghz centrino laptop with 512 RAM).

I did the structure preparations on windows, since I wasn't successful in installing the Chimera program on openSuse 10.2. Still remains a mystery for me up to now.

When you're finished with the preparation, now we can continue to the next step.

2) Sphere generation and selection
For generating the molecular surface of the protein, you will need a program called dms (as I have mentioned in my previous post). Installation was quite simple. Just type “make install” in the dms directory and stop there. You should have dms installed on your system (that's what happened to me in openSuse anyway). Remember that this is installation for a local machine. For parallel machines, there are other things you need to modify (check the dms readme that comes with the package).

When finished generating the molecular surface, use the program sphgen to generate the spheres.

Tip 1: copy the programs you want to use in your working directory!!.
Tip 2: in openSuse, instead of just typing “sphgen (options)”, I had to type “./sphgen (options)” to get it done!

After finished generating the spheres, now it's time to select the spheres you want to use as the active site. You can use the largest cluster created by sphgen, use a sphere in a selected radius, or select the spheres manually. I would recommend the second choice (use a sphere in a selected radius). Here, you should use the mol2 structure of the ligand bound to the pdb protein's active site (mentioned in step 1). This will save you precious time, believe me!

3) Grid generation
For this part, I had no problems at all. I just followed the tutorial, and I was home free.

4)Docking
There are 2 main ways of docking. First is the flexible ligand docking, and second is the rigid ligand docking. The flexible docking lets dock change the ligand conformation in response to the binding site. The rigid ligand doesn't let dock change ligand conformation. You should choose the one which suits your need.

For the docking process, thankfully I had no problems (I used flexible ligand docking). However, you might want to check the parameters that you need to tamper. For docking, I followed the dock v5.2.0 tutorial which is also available at the DOCK website.

Interpreting results
There are two main results that I found interesting (well, up to now, these are the only things I can analyze =)). First is the interaction energy of the ligand-protein complex. The lower the interaction energy, the stronger the bond is. I found this as additional data to supplement my kinetic experiments. Second is the conformation and orientation of the substrates in the binding site. Comparison with established ligand-protein structures can give better understanding on the effect of binding site structure has on substrate binding.

Well, this is a little taste of what DOCK can do for you. I have still much to learn about docking. But, since I am quite sure that it will be very important in future enzymatic studies, I have to spend more time to study it.

The Art of FREE Molecular Docking (Using DOCK 6.1) (Part 1)

Introduction and Installation

Enzymes play an important role in living organisms. They catalyze chemical reactions, where a substrate is converted into a product. Substrates are molecules that bind into the enzyme's active site where it undergoes conversion into the enzymatic product. I am not going to go too deep regarding enzymes, since you can find similar resources for this in the Internet (Wikipedia is a good place to start off).

What I am going to talk about, is a pragmatic way to better understand the interaction between an enzyme and its substrate using molecular modeling, in this case, docking using DOCK 6.1 (check the DOCK website at: http://dock.compbio.ucsf.edu). Well, mostly, I will be talking about my experience using the program, from installation to the docking process.

So what is docking?
Substrates, as do all molecules, have many different conformations they can take. The conformations play a determining factor in the way it binds to the active site of an enzyme. What also needs to be elucidated is the binding orientation, interaction energy (Ei), etc. One way to predict the orientation, conformation, and interaction energy (Ei) of an enzyme-substrate complex, is by molecular docking using in silico (computer) analysis. In short words, docking is meant to see the interaction between molecules and ligands (enzyme or protein). In my case, the data retrieved will then be analyzed to see substrate preference of the enzyme tested.

There is a wide range of programs that can be used for molecular docking, from freeware to expensive commercial wares. Among all, GOLD and Glide are considered to have the best accuracy. But to obtain one of them, you will need to invest at least around 3.200 USD. Too expensive for a student like me, and my lab hasn't allocated that much money to buy softwares. Anyway, for the solution, I tried to search for freewares. To my surprise, I found a lot of docking freewares. Among them are ArgusLab 4.0, Autodock, and DOCK.

At first, I tried ArgusLab 4.0, which was fairly easy to use. Installation was easy (it runs on windows XP), it has a nice GUI, and accompanied with an easy step by step tutorial, I was able to complete the docking process in no time (you can check out their website: http://www.planaria-software.com). However, the software isn't yet recognized in the scientific community. A quick search using the key word “Arguslab” in google scholar only resulted in 66 hits. There is even a comparison of Arguslab with GOLD, which shows that there are many things that needs to be improved in the current Arguslab version. Thus, I moved on to the other options.

Autodock was indeed tempting, however, the procedures to obtain a copy was somewhat “difficult”. You will need to send a fax or mail with the head of your institutes' signature on the license agreement. I am studying in Japan, and it takes time to complete procedures like that. That's why I moved on to DOCK 6.1. It wasn't hard to obtain, since you only have to fill in an on line request (with permission of your supervising Professor) to get it. I got the software after 2-3 days of my request. Lighting quick response.

So, I got the software, now what? Install it right? Well, it turned out not as easy as I suspected. To install DOCK, you will need a UNIX like environment. On windows, you can use a program called CYGWIN, which generates a UNIX like environment in windows. However, I opted to install openSuse linux (which is UNIX based) on my computer (I had a double OS booting). I compared the docking performance on both (cygwin and linux), and found that it was much more stable using the later (linux). The installation itself was sort of a trial and error process. You will need to install the compilers and other programs that are required to use DOCK (check the tab “dock related links” on their website). For a tutorial on installation of DOCK, you can see the DOCK manual (you will need to improvise though). I will make my own step by step installation soon.

Finished installing, you will have all the programs that you need in the /bin/ directory of your installation directory. However, you will need another program called “dms” (to compute molecular surface), which is not included in the DOCK package (you can get dms from: ftp://ftp.cgl.ucsf.edu/pub/dms.zip). I'll give details on installing it later.

There are 4 steps in docking with DOCK, which I will mention in my next post.

Who Took the Third Loaf of Bread?

I just heard this story from Yusuf Estes's site (www.shareislam.com), and find it interesting. The story was about Isa (Jesus) (Peace be upon him) and his companions during a journey. I hope we can all benefit from the moral and logic of the story.

Isa along with his companions were on a journey. During their journey, Isa, gave one of his apostles money and ordered him to buy some bread for their meal. The apostle did what Isa had ordered him to do and bought 3 loaves of bread for them to eat. However, the apostle was somehow afraid of not getting enough to eat, so he took the third loaf of bread and ate it for himself.

The apostle went back to Isa and gave him the 2 loaves of bread remaining. Isa, even though not knowing how many loaves of bread were bought, asked the apostle, “Where is the third loaf of bread?” The apostle replied, “There is no third loaf. The money was only enough to buy two.” Isa didn't reply, and all of them ate the two loaves of bread together.

In the middle of their journey, Isa and his companions hunted a deer. They killed the deer and they cooked it. While they were eating, Isa asked Allah to revive the deer. Just like that, the deer was revived and it jumped and ran away from them. And then Isa asked the apostle (who lied) again, “By the name of The One Who revived the deer, where is the third loaf of bread?” The apostle stood firm and replied, “There is no other loaf of bread, there were only two.” Again, Isa did not reply and they continued the journey.

Soon afterwards, they came to a flowing river. Isa asked his companions to hold his hands. Together, they walked on the water surface and crossed the river! Everyone was bemused. And once again, Isa asked the same apostle, “By the name of The One Who supplied this miracle, where is the third loaf of bread?” The apostle gave the same answer, “There was no third loaf of bread.” And again, Isa didn't reply and they continued their journey.

This time, they reached a dessert. Isa gathered 3 rocks, and asked Allah to turn them into gold. Isa gathered two huge chunks of gold and said, “We will divide this among us, and the one who took the last loaf of bread may have the third all to himself.” Voluntarily, the apostle who lied all along said, “It was I who took the third loaf of bread, so it is my right to have the last chunk of gold.” Isa then replied, “You can take all three, but you are no longer welcomed in this party.” The apostle (now ex-apostle) was so happy to receive the gold, that he didn't care about what Isa told him. He didn't even realize when Isa and the companions left.

While the ex-apostle was admiring the gold and dreaming about his future plans with it, three robbers spotted him. They stole the gold, and in the process, they also killed the ex-apostle. Afterwards, one of the robbers asked the other to buy some bread for them to eat. So off he went to buy bread (no, he didn't eat the bread). But greed whispered into his heart and he plotted to take all the gold for himself. How? He poisoned the bread that he bought. But little did he know, the other two robbers also plotted to take the gold for themselves, and planned to kill him. When the one who bought the bread came, the other two jumped him and killed him. In their joy, the two remaining robbers ate the bread (which was poisoned by the way) brought by the one they killed. And soon after, they died as well.

Soon after, Isa and his companions passed that spot and saw the dead ex-apostle, the three dead robbers, and the three chunks of gold. Isa as. then said, “This is what happens if you seek for worldly goods in life.” The gold was useless, and rather than doing good, it brought the death of the people who desired it.

Is bread worth "killing" honesty?

Is God still divine for us in life? In the world we know today, riches, money, a full tummy and other worldly goods are so tempting and virtually irresistible. We see many people sacrifice everything to get them. When we do get them, we always ask for more and more. Satisfaction is hard to achieve. And worst problem is that they become much more important than honesty, nobility, others lives, and even God Himself. I hope we are all among the ones who receive guidance, and be able to see the truth...

The Dajjal Inside of Us

Dajjal is a well-known character in the Islamic religion, which betrays the truth and sucks people in towards his defiance. Whether he is a real person or a system remains debatable. Christians may also know him as the “anti-christ”. He is said to be one of the signs of “the last day”.

The most dangerous of his characteristics is his ability to mislead people to think that good is bad; heaven is hell, and vice versa (he is also known as “the great deceiver”). However, if we open our hearts and be truthful, we will be able to identify Dajjal’s traps and stay away from them.

The 1 dollar one-eyed pyramid. The symbol of Dajjal??

The modern way of life demands us to reach for a successful career, power, plenty of riches, fun all the way, and other worldly pleasures, a one-dimensional view, which is an analogy of Dajjal’s one eye. Although at times we realize that we are lost and need a more proper goal in life, the pressure that is created around us by Dajjal’s system, forces us to go back to our “ordinary” lifestyle. As we get sucked in his defiance, we get more and more comfortable with the ride and tend to just play along. This way, our happiness will be illusive and short lasting.

Somehow, we have let him taken control of us. His clutches are so powerful that we have let little Dajjals grow inside of us now. His lust, his ambition and his spirit to create a world of ignorance, competition, pragmatism, and materialism have become what we breathe for. We live day by day to continue our routines without any real meaning in what we do. We do our best to improve our way of living, our comfort, yet we tend to forget/ignore what is happening around us.

How can we bear following tomorrow’s fashion trend, while there are still people that don’t even wear clothing? How can we still enjoy juicy thick beefsteaks while there are people that are dying because of hunger?

Still fancy yourself a luxurious dinner? Think again...

Is there no hope left? After these little Dajjals grow inside of us, is there any way to get rid of them?

Let us try to listen to our hearts more intensively. Seek what real happiness is, and let us break free from Dajjals clutches...

The Forgotten Republic of Indonecia

Even though my word processor gave a red underline for the title I wrote, suggesting that it is a spelling error, I can assure you it isn’t.

I took this photograph below when I picked up my wife at Kansai International Airport (Japan) in 2006 (I don’t know whether they have changed it or not). I don’t think that there is an airline called Garuda Indonecia. So, the sign must have meant Garuda Indonesia, but was miss spelled. A funny thing to encounter in an international class airport, and you don’t expect the Japanese to make many mistakes.

Fly with Garuda Indonecia?

The miss spell is kind of ironic, because the Indonesian – Japanese history is quite tied up to each other. Especially if we go back to 62–65 years ago (1942-1945), when the two countries were very “intimately” connected. The sad fact is that, even though most Indonesians are well aware of what happened then, not all Japanese are (maybe because they don’t teach “negative” history subjects in schools).

Is Indonesia that easy to forget?? :P

Global warming and thinking green

Global warming is no longer a POSSIBLE phenomenon. Global warming is already here, it's real and it’s happening at the point of “no return”. Global warming is happening presumably due to the accumulation of CO2 and other green house gases in the atmosphere. An article in Independent online published in February 2006, said that the global amount of CO2 in the atmosphere is already above its threshold, which is 400 ppm. Shockingly, the predicted amount (the time the article was published) was already 425 ppm. Whether we like it or not, we are now facing a time where the unpredictable will most likely happen.

The earth is changing...

In the past year, slight climate anomalies have happened all across the globe. Heat waves, hurricanes, melting ice caps, endless rain, and warm winters (no snow!! Can you believe that?), are all just glimpses of what might come to happen next. By 2100, the global temperature is predicted to rise up to 6oC with a 58-centimeter rise in sea level. In their recent report, the Intergovernmental Panel on Climate Change (IPCC) has charged MANKIND as the guilty party. So what's new? The question is, how did we do it, and what can we do now?

Plants are key organisms in maintaining our climate, because, along with several microbes, they are the only ones who can convert CO2 efficiently into Oxygen. Thus far, most of us have neglected the importance of plants in maintaining our way of life. From 1990 to 1997, every year we lost forests equal to 8285714 football (not American) fields. It means that every hour from 1990 to 1997, we lost forests equal to 945 football fields. The destruction nowadays might be even vaster. This amazing phenomenon itself is more than enough to cause the so-called global climate change (Not to mention the extensive CO2 released to the atmosphere by human activity, and other causes).

Our number one life supporter

Plants are invaluable to us. We have to be more aware of that. They are the only ones who can convert the sun’s energy to be able to be enjoyed by other beings, convert CO2 into oxygen that enables us to live, to breath and of course keeps CO2 from accumulating in the atmosphere (which is the main cause of global warming). From now on, it would definitely help if EVERYONE started thinking “green”. Protecting them means protecting us. Planting and growing them means investing for our future. And being aware of their condition means being aware of life itself. If all of us think "green", I’m sure we can make a difference.

Our Fortressed Education

For me, the ideal goal of “education” is to create minds that will build the community (or at least not burden it). When I say ideal, I truly hope that one day, it can be more than just a jargon. The prosperity and downfall of a community depends on the quality of its scholars. And the quality of a community’s scholars depends on the education they undergo. Wouldn’t it be nice if a community had bright scholars that are committed and focused on its development? But how can a scholar focus on building his community if he doesn’t know, doesn’t understand, and doesn’t feel connected to it?

The educational system in Indonesia (formal and informal) isolates the scholars from its community. It acts like a fortress that separates the so-called “intellectuals” and the so-called “people”. Once the “intellectuals” go back to the community, they are placed in places that are somewhat isolated from the “people”, where they gather with their same kind, thus forming a golden cage, which they enjoy by themselves. The “people” on the other hand, do not receive any benefit from the “intellectuals”, which they actually supported to flourish (indirectly).

Trapped by their state of mind, the “intellectuals” are then ignorant and have no significant role in the community’s development, which in turn makes the community stagnant (or even worse, degenerate), which might possibly be happening in Indonesia right now…

Let’s find the key to release our fear and ignorance, and let us regain our strength and courage to do what we think is right.

Nevertheless, I am pretty sure that many of Indonesia’s scholars have found that this mind cage does really exist, and are in the middle of finding the key to unlock it. I hope we can all contribute towards a better future for the people who need it (in any way possible).

Welcome My Son!!

Finally, after a fierce struggle of life and death, my wife gave birth to our beloved son. Welcome to this colorful yet challenging world“Saifan Seigi Ragamustari”!
I can’t say I have ever felt this happy, exited, and scared before.

We hope you grow up to be a good, kind, and strong person, and close to Allah nevertheless. And may Allah give my wife and me the power and strength to be good parents in every way.

He was born on the 14th of January 2007, 11.04 Japan time in Uji byouin (uji hospital), Uji, Kyoto, Japan. His birth weight was 2.922 kg, with a length of 48 cm.

Saifan and Mommy

Thank you Allah our dear lord. For giving us happiness and blessing through out our entire lives (Even though we tend to forget the good things and remember the bad things, lets stop doing that). Please pray for us my dear friends.

Once again, Welcome my son!!

The death of young potency

Being a youngster in a community isn’t always an advantage, especially in Indonesia. Sure, you get to be guided, taught, and somehow given less responsibility. But you sometimes do not get the respect and the acknowledgment you deserve. Older people tend to have delusions of grandeur that they are more experienced, smarter, stronger and wiser, and therefore deserve to have more respect than their younger counterparts. It seems like the younger you get, the less respect you get.

No respect means non-equal opportunities, and it is indeed a character killer. You are disregarded of your opinions, your ideas, your arguments, and abilities. Even though yours might be better.

Most Indonesians experience this at a very young age, where the older person is the teacher. Yes, at school. Teachers are never wrong. They are always right even though they are wrong. You aren’t supposed to draw a car jumping off a cliff, spiderman, a clown, etc. You are supposed to draw two mountain peaks, a road in the middle, and some paddy fields (the typical drawing of an indonesian youngster). You aren’t supposed to challenge your teacher’s ideas, if you don’t want to get bad grades. Don’t get me wrong. I respect my teachers. I am who I am partly because of them. But frankly, what teachers are doing nowadays is character killing, and what’s worse is that it’s contagious, and passed on to the next generation. It makes people blunt, dependent, scared (to express ideas) and uncreative. We need a way of teaching that “guides” yet not dominates.

This kind of “age superiority” is apparent in almost every aspect of an Indonesian’s life. In the politics, in the university, in business, and almost in everything else. The only thing that overcomes the dominancy of age, in most cases, is money (I guess).

By inhibiting growth and expansion of young, fresh, and not yet corrupted minds, the potency it has is slowly degraded. And the death of a nations young mind is death to the nation itself. This might explain why Indonesia is so fragile.

Let's become their guide and their inspiration

Nevertheless, what good can we do rather than by starting with ourselves. May we be among the people who respect their young, yet become their guide and their inspiration. (Gee, how will I be when I get old? Like I’m not old already :D)

Belajar Tuma'ninah dari Orang Jepang

Sambil menyelam minum air
Sambil mengerjakan pekerjaan rumah, sambil makan dan main komputer.

Melakukan beberapa hal secara bersamaan, bagi saya (dan mungkin banyak orang) sudah menjadi warna yang tidak bisa dihapus dari kehidupan sehari-hari. Ketika kita melakukan banyak pekerjaan secara bersama-sama (yang diwarnai dengan keterburu-buruan), apakah hasil yang diperoleh akan maksimal?

Di jepang, saya diingatkan kembali akan pentingnya tuma'ninah. Tuma'ninah saya pelajari pertama kali sewaktu di SD (waktu pelajaran shalat). “Lakukan semua rukun shalat dengan tuma'ninah”, begitu kata buku yang saya baca (seingat saya...). Tuma'ninah di sini berarti melakukan setiap rukun shalat dengan berurutan, tertib, dan benar-benar fokus. Tuma'ninah semacam inilah yang berhasil diadopsi orang jepang di dalam kehidupan mereka sehari-hari.

Kebanyakan orang jepang (biasanya) fokus melakukan satu pekerjaan saja di dalam satu waktu. Maklum, mungkin karena ga terlalu banyak yang dipikirkan kayak kita orang Indonesia. One things at a time, begitu kata orang bule. Pekerjaan-pekerjaan lain akan dilakukan setelah pekerjaan yang sedang dia kerjakan benar-benar tuntas. Setiap pekerjaan yang dilakukan mendapatkan perlakuan ekslusif, sehingga hasilnya benar-benar maksimal. Kira-kira begitulah tuma'ninah ala orang jepang.

Seharusnya, bagi seorang muslim, paling tidak 5 kali sehari ia diingatkan atau dilatih untuk tuma'ninah, yaitu di dalam shalat (pelajaran kelas 3 – 4 SD sih... saya juga sudah ga terlalu ingat). Tuma'ninah merupakan salah satu kunci untuk mengalami shalat yang khusyuk, shalat berkualitas tinggi. Sudah sepatutnya setiap muslim mencoba dengan sekuat tenaga untuk menggapai kekhusyukan di dalam shalat. Sayangnya, karena adanya desakan-desakan duniawi (dikejar deadline, ada rapat, ada kelas, dsbg), terkadang sulit sekali untuk melaksanakan shalat secara tuma'ninah. Ketiadaan tuma'ninah di dalam shalat menghasilkan keterburu-buruan, bacaan yang super cepat (sampai-sampai lidah tidak mampu mengikuti), menjamak shalat yang masih bisa dikerjakan pada waktunya, lupa jumlah rakaat, dll. Pada akhirnya, kekhusyukan tidak tercapai, dan shalat hanya menjadi sebatas gerakan-gerakan yang kosong tanpa makna. Bagaimana shalat yang semacam itu bisa menjadi tiang agama? Oleh karena itu, selagi berusaha, mari terus berdoa semoga kita semua diberi kemampuan untuk tuma'ninah dan mencapai shalat khusyuk.

Intinya, ketuma'ninahan menjanjikan kemungkinan lebih besar untuk mendapatkan keberhasilan / hasil berkualitas tinggi di dalam menyelesaikan suatu tugas atau pekerjaan. Seorang tukang martabak pun menggunakan tuma'ninah sebagai kunci kelezatan martabaknya (urutan cara mengolah adonan sampai ke cara memasaknya). Maaf lari ke martabak, habis, rindu banget sama martabak air mancur sih.

Orang jepang bisa melakukan segalanya secara tuma'ninah. Kita, seharusnya bisa juga!!!

Bang, SMS Siapa Ini Bang?

Bukankah merupakan suatu keanehan/anomali apabila lagu “SMS” oleh Ria Amalia begitu bombastis? Dari semua yang ditawarkan oleh lagu tersebut (baik iringan musik, lirik, video clip, dll), bagi saya, semua biasa-biasa saja, alias tidak ada yang istimewa (silakan lihat video klip-nya melalui link di bawah). Walaupun tidak memiliki data akurat, melalui blog teman2, status teman-teman di YM, berita online, mailing list dll, tersirat bahwa lagu tersebut telah menarik jumlah pendengar yang cukup fenomenal. Bahkan, kabar terbaru menyebutkan bahwa sekarang, lagu tersebut sudah dibuat jawabannya!! Hadirnya lagu jawaban menandakan bahwa lagu pendahulu telah laku keras di pasaran (Ada yang tahu lagu Betharia Sonata yang berjudul “hati yang luka”?).

Sudah seberapa luas teknologi SMS digunakan??
Lagu SMS dapat menjadi semacam Indikator

Sebab-sebab yang (mungkin) menjadi pendukung fenomenalnya lagu SMS tersebut adalah kenyataan bahwa kehidupan bermasyarakat di Indonesia sudah begitu lekat dengan apa yang menjadi tema lagu tersebut. Dalam kenyataannya, salah satu tema lagu tersebut, yaitu ber-SMS, sudah tidak dapat dipisahkan dari kehidupan bermasyarakat. Selain membawa tema SMS, lagu tersebut mengusung tema-tema lain yang membawa pendengar merasa lebih terlibat lagi. Kejadian pernah salah kirim SMS, atau salah dikirimi SMS memang sangat sering terjadi belakangan ini. Apalagi kalau sudah melibatkan perasaan. :P

Bagaikan gen tumor yang membuat sel tumor membelah cepat tanpa henti, faktor-faktor tersebut menjadi katalis yang membuat lagu SMS semakin hari semakin meraup banyak penggemar. Orang merasa terlibat, terkait dan tergelitik oleh lirik yang dilantunkan oleh Ria.

Jumlah pendengar lagu SMS yang semakin membengkak
bagaikan sel tumor yang sedang membelah (dari history.nih.gov)

Sebagaimana telah saya sebutkan, “booming”-nya sebuah lagu di pasaran dapat menjadi indikator mengenai apa yang sedang terjadi di masyarakat. Dalam kasus lagu SMS, indikasi bahwa masyarakat kita sudah lekat dengan SMS mungkin tidak perlu terlalu dikhawatirkan (walaupun efek ketergantungan terhadap apapun, termasuk teknologi, kemungkinan besar memberi efek negatif. Contohnya adalah dapat membuat kita menjadi lebih malas). Yang perlu dikhawatirkan adalah apabila tema-tema negatif yang diusung oleh lagu tersebut (dan lagu-lagu lain di pasaran) ternyata sudah begitu mendarah daging di masyarakat...

Nah, apakah kamu menganggap “booming” lagu SMS tersebut sebagai suatu keanehan/anomali?

:D

Belum lihat video clip dan dengar lagunya? Klik di sini

Merdeka KAH???

Pada tahun 1945, setelah 3,5 abad lebih mengorbankan darah dan jiwa, akhirnya bangsa Indonesia berhasil memproklamasikan kemerdekaannya dari belenggu penjajahan. Momen status quo (ketika Jepang menyerah kepada sekutu) dimanfaatkan secara manis oleh bapak-bapak proklamator kita.

Proklamasi Kemerdekaan Republik Indonesia

Setelah 61 tahun proklamasi kemerdekaan diserukan, sudahkah kita, bangsa Indonesia, benar-benar merdeka? Sudahkah kita benar-benar lepas dari penjajahan negara lain? Sudahkah kita merasa bebas dan nyaman melakukan apa yang kita yakini benar? Sudahkah kita memaknai dan menjiwai arti “merdeka” di dalam kehidupan kita sehari-hari? Mungkin kebanyakan dari kita akan menjawab dengan “belum”.

Walaupun saat ini kita tidak dijajah secara fisik oleh negara lain (seperti saat kita dijajah belanda dan jepang), sadar tidak sadar, banyak belenggu-belenggu lain yang mengekang kita, yang membuat kita tidak merdeka secara nyata, alias terjajah.

Satu bentuk keterjajahan di Indonesia yang sudah cukup parah adalah terjajahnya pola pikir. Yaitu ketika pola pikir kita membuat kita terbelenggu dan tidak bebas. Keterjajahan pola pikir ini terjadi akibat banyak hal, diantaranya oleh: lingkungan sekitar kita, keluarga, media, dan lain lain. Salah satu contoh nyata yang paling jelas dan destruktif adalah pola pikir yang membuat kita begitu tergantung kepada uang dan materi (materialisme). Uang dan materi menjadi parameter dan sistem nilai di dalam semua sektor hidup. Baik di dalam memilih pekerjaan, persiapan berumah tangga, memudahkan birokrasi, bahkan di dalam berbuat kebaikan sekalipun (semakin banyak uang yang dikeluarkan untuk tujuan kebaikan, semakin dihargai kebaikan tersebut). Pola pikir ini menjadikan ruang gerak kita terbatas hanya di dalam kerangka ke”uang”an. Pola pikir seperti ini pula yang menjadikan negara kita keropos oleh korupsi.

Merdeka secara nyata adalah ketika kita mampu menegakkan kebenaran yang kita yakini dengan sebaik-baiknya, tanpa ada perasaan takut atau tidak nyaman. Dan kemerdekaan seperti itu saat ini sulit dirasakan oleh kebanyakan rakyat kita yang masih dililit kesulitan. Satu cara untuk mendobrak belenggu penjajahan adalah dengan (meminjam istilah Ali shariati) melakukan hijrah. Hijrah dari keburukan kepada kebaikan, hijrah dari pemikiran kita yang lama ke pemikiran yang baru. Hijrah dari semangat yang keropos ke semangat yang baru. Dengan hijrah, kita bukan sekedar melarikan diri dari belenggu-belenggu yang mengekang kita, namun melakukan persiapan yang lebih mantap untuk kelak melawan belenggu-belenggu tersebut. Sama halnya seperti hijrah Rasul dari Mekkah ke Madinah. Beliau bukan sembarang melarikan diri, tetapi beliau membentuk fondasi yang kuat untuk melawan kelaliman. Proklamasi Kemerdekaan Indonesia mengandung makna yang kurang lebih sama.

Kembali lagi ke fenomena 17 Agustus. Yang dominan terjadi pada tanggal tersebut adalah pesta-pora, lomba-lomba dan bersenang-senang. Sebenarnya tidak ada yang salah dengan meluapkan kegembiraan, asalkan tahu betul sebabnya. Sayangnya, introspeksi akan makna yang ada dibalik proklamasi kemerdekaan itu sendiri menjadi sisi yang kurang populer. Jika pola pikir semacam ini dibiarkan berlanjut, semakin lama hari kemerdekaan akan semakin menjadi sekedar rutinitas belaka yang maknanya semakin terlupakan. Oleh karena itu, menyambut ulang tahun kemerdekaan Indonesia yang ke-61 ini, mari kita kembali hijrah dan membangun semangat baru untuk berbuat yang terbaik bagi bangsa pada umumnya, dan diri kita pada khususnya.

Hancurkan belenggu-belenggu zaman yang melumpuhkan kita!!!

MERDEKA!!!

The Untouchable Israel

OK, so Hizbullah kidnapped 2 Israeli soldiers to ask for a trade for their own men. And now Israel have responded in fashion. After dozens of air raids (which killed many civilians I might add), the latest news is that 8000 Israeli troops have raided Lebanon in continuation of their effort to neutralize the Hizbullah forces.

Great job Israel!! The enemy is surely going to be crushed by your sublime power and strength!! You guys are doing a wonderful job so far... In killing the CIVILIANS and CHILDREN I mean (as the 828 people killed are mostly civilians and children, with more than 3000 injured). And not to mention blowing away peoples houses to bits so that they won't have any place to go home to. And of course your success in VIOLATING COUNTRY TERRITORY BORDERS. Who the hell are you guys fighting? Hizbullah or THE LEBANESE PEOPLE?!!

There definately has to be civilians trapped in a blow like this (Picture courtesy of Yahoo News)

Hey America and UN!!! Continue to support Israel OK? You guys are doing a fantastic job... No need to issue an immediate ceasefire. Rice is right (or is she?)!! A cease fire will just INCREASE THE TENSE AND THE KILLINGS! Everybody stupid enough (including Rice) knows that cease fires are used to ignite larger war, and not to stop the ongoing one (yeah right...) . Let the people die at this rate. No need to change the death rate, or more else stop it.

For the rest of the world (including me of course), the only thing we can do now is to grumble, watch and of course pray for everyone's best and so that we will all learn from this international tragedy... As we all know, in the time being, most of us are helpless.

A MILITARY AGGRESSION towards another country in order to eliminate a group of criminals (depends on your point of view) is justifiable to protect the people of your own country. The hell with the people living in other countries. They are just not that important!! They are dispensable!! Isn't that right!!?? KILL KILL and KILL.

And so, another military aggression has been launched, and the culprit will almost definitely get away with it. Because we all know that there are several untouchables in the worlds political stage, which can get away with almost everything they do. And Israel is among them (guess the other one yourself). After Iraq and Lebanon, who will come next? Iran? North Korea? Or maybe even Indonesia? Watch out world...

One of these baby's might be heading in your direction someday (Picture courtesy of Yahoo News)


OK, enough with the sarcasm... I'm getting confused myself.

I'm not a political analyst and I may not have the qualifications for writing an analysis on this matter, I just need to get the emotion out. What I know is that WAR is WAR and we should do everything in our powers to stop it.

May our Lord give us the ability to see the good, the hikmah and the lessons in everything that happens around us. And may our Lord give blessing towards all the people in repression, in their life and in their death....

Go here to get a better view on the topic

Sembuhkan Penyakit Negativisme!!!

Setelah cukup lama merasa gundah dan gelisah, akhirnya ketemu juga biang keladinya. Ternyata pikiran dan hati ini telah terjangkit penyakit negativisme. Hal ini terjadi ketika semua yang dilihat dan dirasakan lebih menghasilkan efek negatif (kesal, marah, sedih, kecewa, dan sejenisnya) ketimbang efek positif (bersyukur, bahagia, dan sejenisnya). Bagaimana mau mewarnai dunia ini dengan kebaikan dan kebahagiaan kalau diri kita sendiri didominasi hawa negatif? Saya asumsikan kita semua memiliki pemahaman yang sama akan makna kata “negatif” di sini: semua mua yang sifatnya ga baik…

Manusia akan melihat, merasakan dan menginterpretasi fenomena-fenomena yang terjadi di luar dirinya sesuai dengan apa yang ia rasakan di dalam dirinya. Apabila jiwa seseorang dipenuhi rasa negatif, maka interpretasi terhadap apa-apa di luar dirinya (lingkungan dan hidup pada umumnya) akan menjadi negatif pula. Segala yang negatif akan menghasilkan hal yang negatif pula. Dalam hal ini, interpretasi yang negatif akan disertai oleh respon yang negatif.

Negativisme akan menjadikan seseorang kerdil dan kurang bermanfaat, baik bagi orang lain dan lingkungannya, maupun bagi dirinya sendiri. Seseorang yang mengidap penyakit negativisme, secara tidak sadar akan melakukan perbuatan yang negatif juga. Ngomongin orang, menilai orang secara sepihak, mudah marah, dsbg. Perbuatan negatif apa yang memberi kebaikan bagi seseorang, orang lain, dan lingkungan sekitarnya? Jawabannya: tidak ada.

Sudah selayaknyalah kita selalu berusaha untuk bersikap positif. Bersikap positif / positivisme akan menyembuhkan penyakit negativisme. Kita akan merasa jauh bahagia dengan positivisme. Apabila kita mampu memandang segalanya dengan positif, niscaya semua tindakan yang kita lakukan akan menjadi positif juga. Ingat terus bahwa kebaikan hanya akan menghasilkan kebaikan, walau terkadang tidak sesuai dengan harapan kita.

Siklus positivisme (http://www.theconsultingrooms.co.uk)

Untuk membangkitkan positivisme dan membunuh negativisme, ada beberapa kiat yang mungkin bisa efektif. Diantaranya adalah:

1. Senyum!!!

2. Jangan punya prasangka buruk kepada makhluk Allah yang lain. Karena, apabila kita berburuk sangka kepada makhluk Allah, secara tidak langsung, kita telah berburuk sangka kepadaNya juga.

3. Gantungkan seluruh harapan kita kepada Allah semata. Harapan lah yang membuat seorang manusia menjadi lebih tegar di dalam menghadapi hidup. Dan tidak ada tempat menggantungkan harapan yang lebih kuat lagi dibandingkan Sang Pencipta.

4. Lain lain (boleh diisi sendiri deh…)

Bagi yang mengidap penyakit negativisme, ayo kita sama-sama sembuhkan. Dan bagi yang sudah sembuh, perkuat lagi antibodinya agar tidak terjangkit penyakit yang sama. Semoga dengan positivisme kita mampu mewarnai dunia dengan warna-warna yang cerah.

C'mon, let's be positive!!!

Special Thanks to the South African guy who presented a heart moving Khutbah which inspired this writing. I didn’t have the chance to thank him in person, I just hope Allah blesses him in whatever he does.

Bagaimana Pola Pelipatan Protein?

Tau ga, protein (yang katanya penting), dibentuk oleh kombinasi 20 macam asam amino yang berbeda. Pola-pola bergandengan asam2 amino tersebut bisa bermacam-macam. Ada banyak kombinasi yang bisa terbentuk. Anyway, satu fenomena di dalam dunia protein-perproteinan, yang tidak kunjung mampu dijawab oleh manusia sampai saat ini adalah fenomena pola lipat-melipat. Protein, khususnya enzim, melipat dan membentuk suatu daerah yang dinamakan “active site domain”. Kenapa dinamakan active site? Karena orang meyakini bahwa daerah ini memiliki fungsi spesifik yang mengaktifasi atau menon-aktifasi reaksi-reaksi tertentu.

Struktur2 protein, dari yang linear sampe yang nglipet-lipet

Ga ngerti? Sama. Saya juga ga terlalu ngerti kok. Cuma karena disuruh baca sesuatu sama sensei, mau ga mau harus mencoba dan memaksakan diri untuk mengerti (yang sampai sejauh ini belum berhasil aja). Yang jelas, sekali lagi, sudah cukup lama orang berkutat mempelajari si protein. Perlu diketahui seluruh proses pembentukan tubuh kita dibantu oleh protein. Protein lah yang diyakini sebagai hasil akhir dari proses penterjemahan gen. Proses pembentukan hidung anda yang mancung, mata anda yang sipit, kulit anda yang coklat, dll, semua adalah campur tangan si protein (dan Tuhan juga tentunya).

Sesuai dengan judul, balik lagi ke fenomena lipat melipat di dalam struktur protein. Fenomena ini sudah diteliti selama kurang lebih 25 tahun lamanya. Tapi orang tetep ga tau dan ga bisa memprediksi pola pelipatan protein. Jadi suka-suka dia aja mau melipat kayak bagaimana…Walaupun sekarang fenomena ini belum mampu dijelaskan, suatu saat nanti, kemungkinan besar manusia akan bisa menjawab bagaimana pola fenomena ini terjadi (manusia gitu loh).

Setelah nanti si bang orang tahu gimana pola si protein melipat, apakah umat manusia akan menjadi lebih bahagia???

BTW, setelah baca ini, jadi tahu ga jawaban dari pertanyaan yang sekaligus jadi judul di atas?? Hehe....

Para Pendosa

Siapa sih yang tidak pernah melakukan dosa atau kesalahan?
Jawabnya tidak ada. Semua pasti pernah melakukannya. Karena manusia memang tempatnya salah, lupa dan dosa. Termasuk saya, dia, mereka, dan juga anda. Jadi kesimpulannya, semua manusia adalah pendosa!!!

Diantara manusia-manusia pendosa di seluruh dunia, ada manusia-manusia yang sudah tidak peduli dan tidak peka terhadap kesalahan-kesalahannya, namun ada juga sebaliknya. Manusia yang peka terhadap kesalahan-kesalahannya dan senantiasa bertaubat dan memperbaiki diri.

Taubat dan kemauan untuk selalu berusaha memperbaiki diri adalah yang membuat seseorang lebih baik dari orang lain. Semoga kita semua diberi kepekaan oleh Allah untuk selalu senantiasa sadar dan mawas diri akan kesalahan-kesalahan kita.

Merasa Lebih Baik dari Orang Lain

Wahai Allah, ampunilah aku dan hamba-hambaMu yang lemah, takabur dan terlalu sering merasa lebih benar dari orang lain. Sadarkanlah dan ingatkanlah kami semua bahwa kami tidaklah sempurna. Kesempurnaan hanya milikMu semata, dan kami benar-benar adalah tempatnya salah dan lupa.

Jangan Menunda-nunda!!

Berbuat baik dan beramal sholeh jangan ditunda-tunda. Begitu kata Bimbo di dalam lagunya “Jangan Ditunda-tunda”. Dan sungguh rangkaian kata-kata tersebut tidak bisa dianggap sepele. Karena apa yang bisa dilakukan sekarang, belum tentu dapat dilakukan nanti. Saya yakin kita semua sadar akan hal ini, hanya sering lupa saja.

Tadi malam Saya mendapat peringatan keras dari Tuhan untuk tidak menunda-nunda. Peringatan yang datang melalui mimpi, namun terasa sangat nyata.

Di dalam mimpi itu, saya belum melakukan shalat wajib. Dan sedang asyik melakukan sesuatu (ga inget juga melakukan apa). Padahal di dalam hati, sudah ada niat ingin melakukan shalat. Namun tidak dikerjakan... karena saking asyiknya. Setelah perkara asyik itu selesai, barulah saya jalan tergopoh-gopoh menuju kamar mandi. Namun ketika akan mengambil wudlu, setelah membuang air kecil (ga penting banget deh), bumi berguncang dengan sangat keras dan dahsyatnya!! Saya yang sedang di kamar mandipun terpaksa mengurungkan niat untuk berwudlu. Gempa bumi kah? Bukan! Jauh lebih dahysat dari sekedar gempa bumi! Tiba-tiba tubuh saya terangkat ke atas lalu terbanting ke bawah bagaikan adonan martabak telur yang sedang diracik oleh si abang martabak (duh... pengen makan martabak nih...). Dan seketika itu pula saya menyadari bahwa KIAMAT telah datang menghampiri. Akhir dari segalanya... Dan saya belum SHALAT!!! Perasaan menyesal yang amat sangat timbul di diriku. Penyesalan yang tidak ada artinya. Karena semuanya sudah terlambat... Damn!

Setelah tahu bahwa itu hanya mimpi, saya sadar bahwa saya telah diberikan kesempatan lagi untuk memperbaiki sikap.

Thank you O God for all of your blessings, which we often fail to see and be thankful of.
Ingat... JANGAN MENUNDA NUNDA!!! (peringatan keras bagi diri sendiri yang masih sering menunda-nunda)

Masih ada waktu untuk memperbaiki diri...
Walaupun kita tidak tahu sebanyak apa injury time yang kita punya.

Hijrahlah!!

Akan tiba saatnya ketika seorang anak manusia merasa stagnan. Entah karena merasa sungguh tidak berdaya dan hampir menyerah, atau merasa luar biasa mapan dan merasa tidak ada yang perlu diperjuangkan. Sifat stagnan akan membuat manusia kehilangan semangat untuk bertebaran di muka bumi untuk mewarnai hidup. Pada masa-masa seperti ini, seorang manusia perlu melakukan hijrah.

Hijrah?... Ya, Hijrah sahabat-sahabatku!!!

Hijrah berarti berpindah. Berpindah dari satu tempat ke tempat yang lain. Berpindah dari satu kondisi kepada kondisi yang lain. Hijrah akan membuat si pelaku hijrah memiliki semangat baru, kekuatan baru, sudut pandang baru, hidup baru. Hijrah akan membebaskan seseorang dari penjara-penjara pikirannya (penjara kultur, penjara sejarah, penjara sistem sosial, dll) Ketika berhijrah, seseorang akan mulai berjuang dari nol lagi. Membuka halaman baru dengan semua yang serba baru.

Rasulullah saw pun melakukan hijrah dari Makkah menuju Madinah. Ketika itu, beliau sungguh ada di dalam tekanan yang amat dahsyat dari kafir Quraisy. Tugas berat (menyeru jalan selamat bagi seluruh umat manusia) masih dipikulnya, namun ancaman pembunuhan membayanginya. Turunlah perintah Allah untuk berhijrah. Meninggalkan tanah kelahiran, meninggalkan harta, meninggalkan semua (yang secara kasat mata) paling berarti.

Peristiwa Hijrah Rasulullah saw tersebut, ditetapkan sebagai dasar penanggalan kalender hijriah. Penetapan kalender hijriah bukan didasari tahun kelahiran Rasul, bukan pula tahun ia wafat. Mengapa? Jawabannya mungkin karena Hijrah-lah yang menjadi titik tolak perjuangan Rasul di dalam menegakkan jalan-Nya. Dengan berhijrahlah beliau mampu mentransformasi Islam menjadi kekuatan yang diakui oleh umat manusia.

Kita harus selalu ingat, bahwa walaupun ada banyak arah dan tujuan, hijrah yang utama adalah hijrah untuk membangun dan memperbaiki diri sendiri demi menggapai cinta sejati, cinta Allah Penggenggam alam semesta, serta menegakkan agamaNya.

Semoga semangat hijrah Rasulullah saw. senantiasa mewarnai jiwa kita semua di tahun baru hijriah ini. HAJARLAH KESOMBONGAN ZAMAN!!!

***Selamat Tahun Baru Hijriah 1427***

Semoga dapat menjadi penyemangat bagi jiwa-jiwa yang sedang lesu (termasuk jiwaku)...

Korbankan "Ismail"mu!!!

Jamarat. Perlambangan Syaitan yang menggoda Ibrahim ketika menjalankan perintah "Korbankan Ismail".

KORBANKAN “Ismail” mu! (terinspirasi oleh “Haji” karangan Dr. A. Syariati)

Ismail adalah anak dari Nabi Ibrahim a.s. Ibrahim a.s. Sangat menyayangi Ismail yang kelak akan juga menjadi seorang nabi. Bagaimana tidak, Ketika itu Ibrahim a.s sudah sangat tua, sedang ia belum juga dikaruniai oleh seorang anak. Setelah berdoa dan berdoa, akhirnya Allah mengkaruniai Ibrahim a.s. dengan Ismail. Sayangnya Ibrahim a.s. kepada Ismail luar biasa.

Idul Adha dan berhaji adalah napak tilas dari perjalanan Ibrahim a.s. ketika menjalankan perintah Tuhan yang sangat berat. Menyembelih Ismail. Di dunia ini, selain Ismail, mungkin tidak ada yang lebih disayangi oleh Ibrahim a.s. Namun Allah memerintahkannya untuk menyembelih Ismail yang sangat ia sayangi. Apa tujuan dibalik perintah itu?

Ibrahim a.s. adalah kekasih Allah. Namun sebagai manusia, ia masih memiliki kecintaan kepada dunia. Kecintaan Ibrahim a.s. kepada dunia termanifestasi pada Ismail. Maka ketika Allah memerintahkan Ibrahim a.s. untuk menyembelih Ismail, sebenarnya Allah memerintahkan Ibrahim untuk mengorbankan kecintaannya kepada dunia. Apakah Ibrahim a.s. melakukannya? Jawabnya adalah YA. Dengan melewati berbagai macam rintangan dan godaan, akhirnya ia melaksanakan perintah Allah. Ismail pun tak kalah tabah dan berserahnya. Keikhlasan Ismail untuk menerima perintah Allah menjadi salah satu kunci keyakinan Ibrahim a.s. di dalam melaksanakan perintah tersebut. Pada akhirnya, Ismail digantikan oleh hewan qurban, dan Ibrahim a.s. tidak kehilangan apapun. Sebagai symbol bahwa kecintaan kepada Allah tidak akan membawa manusia kepada kesengsaraan.

Kisah nabi Ibrahim tersebut seharusnya menjadi contoh bagi kita semua. Di dalam hati kita semua, kecintaan kepada dunia pasti ada. Bahkan tidak jarang kecintaan kepada dunia mendominasi dan mengalahkan kecintaan kita kepada Allah. Banyak orang yang lebih cinta uang daripada Allah. Banyak orang yang lebih cinta perempuan daripada Allah. Banyak orang yang lebih cinta menonton pertandingan liga Inggris di TV daripada Allah (sekedar mengingatkan diri sendiri, hehe..).

Idul Adha adalah ajang yang mengingatkan kita untuk MENGORBANKAN “Ismail-Ismail” kita di dunia. Tentunya untuk menggapai cinta yang lebih mulia. Mengorbankan di sini tentunya simbolis (makanya diberi bold dan italic) Identifikasi apa dan siapa “Ismail”mu, dan jangan biarkan cinta kita kepada “Ismail-Ismail” kita di dunia melebihi cinta kita kepada Sang Pencipta.

*SELAMAT HARI RAYA IDUL ADHA 1426 Hijriah*
Semoga kita selalu senantiasa berusaha untuk menggapai cinta-NYA…