NAMOT Pre-Release 2.2.0-pre4 In OSX 10.8 (Maybe Older Versions)

A recent visit to the College of Nanoscale Science and Engineering (CNSE) at SUNY Albany inspired a few new DNA ideas that I decided would be greatly simplified by having NAMOT available again for design. Having failed at the base install of the NAMOT 2 version and, unfortunately, not having NAMOT available in Fink for a simple installation, the solution became to build the pre-release from scratch. Ignoring the many errors one encounters while walking through an OSX/Xcode/Fink/X11 bootstrap, the final procedure worked well and without major problem. As usual, the error messages at varied steps are provided below because, I assume, those messages are what you’re searching for when you find your way here.

0. Required Installations

You’ll need the following installed for this particular build. I believe XCode is the only thing that you’ll have to pay for (if you don’t already have it. I seem to remember paying $5 through the App Store).

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Finally! A Good Use For The Nano Gallery (Kudos To

An unlabeled version of the fused-diamondoid-carbon-nanotube-van-der-waals-crimp-junction found a home in the NanoSonic Nanotechnology Coloring Book, page 8 (I show it below (with mine shown a little more nano-sized)). I think that’s pretty hip.

Kudos to Tom Moore for pointing it out.

NanoHive@Home’s Published Results (Finally): Analysis Of Diamondoid Mechanosynthesis Tooltip Pathologies Generated Via A Distributed Computing Approach

Published in the Journal Of Computational And Theoretical Nanoscience. This paper has been as delayed in posting as the accepted article was long in printing, which was less time than the wait for the completion of the manuscript, which itself was massive compared to the time of the experiments themselves, which was fractional compared to how long it would have been without the NanoHive@Home crew that donated so much compute time to the project so long ago. First off…


This work would not have been possible without the enormous contribution of the NanoHive@Home participants, composed of over 6,000 worldwide volunteers and their computers.

For those that were part of the NHAH community and want to see what the final work looks like, please drop me a line [] so we can properly settle up.

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Amber And Ubuntu Part 2. Amber10 (Parallel Execution) Installation In Ubuntu 8.10 (Intrepid Ibex) With OpenMPI 1.3… And Commentary

After considerable trial and building/testing errors, what follows is as simplified a complete installation and (non-X11/QM) testing of Amber10 and OpenMPI 1.3 as I think can be procedure’d in Ubuntu 8.10 (and likely previous and subsequent Ubuntu versions), dealing specifically with assorted issues with root permissions and variable definitions as per the standard procedure for Amber10 installation.

I’ll begin with the short procedure and bare minimum notes, then will address a multitude of specific problems that may (did) arise during all of the build procedures.  The purpose for listing everything, it is hoped, is to make these errors appear in google during searches so that, when you come/came across the errors, your search will have provided some amount of useful feedback (and, for a few of the problems I had with previous builds of other programs, this blog is the ONLY thing that comes up in google).

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Metamodern – The Trajectory Of Technology

Eric Drexler is categorically the most knowledgeable and well-rounded scientist I have ever met. Period.

– From an interview with Sander Olsen for, November 2005.

Friend, mentor, and co-author K. Eric Drexler has begun a new blog and I am thrilled to have at the click of a mouse the thoughts of a founding father of my field who remains a strong voice for its progress by seeing beyond the boundaries that define scientific disciplines.

If all scientists had his mastery of insight and interdisciplinary mindset, I dare say we might be done by now.

And I subscribed to the feed, too.

NANONEWS: A Noteworthy Name In Nanotechnology or “I Guess No One Told Them About The Gallery.

From the “It’s my blog and I’ll post if I want to” department, a little bit of free press and kind words came my way a few days back from Kacey Williams of the Taylor & Francis Group/CRC Press in the form of the most recent issue of NANONEWS, the monthly newsletter at In case you’ve not been paying attention, the website recently went very 2.0 in appearance and organization, providing a excellent source of nano-related news from a hard-science perspective (a community-based Eureka Alert as it were).

My CV‘s undergone some much-needed settlement since the bio for the newsletter was provided to the website, but all the science still holds, which is just as it should be.

nanonews feature

A copy of the newsletter is sitting locally for my own documentation at


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sed-Based Script For Converting NAMOT And NAMOT2 DNA Output To ffAMBER Format For GROMACS Topology Generation v1

In continuing efforts to streamline the simulation of atomistic DNA structures in GROMACS using the ffAMBER force field (the port of AMBER for GROMACS), the following script takes the .pdb output of NAMOT or NAMOT2 and does all of the atom label and atom label position conversions, correct 3′ and 5′ terminal H atom assignments, and random changes throughout the .pdb file to provide something that should flow seamlessly into GROMACS.

“Did you need to post the entire script and not just provide the downloadable text file as a link?” Of course, as I suspect no small number of people looking for how to convert a NAMOT pdb file into ffAMBER-speak will begin by searching based on GROMACS errors, which occur one missing residue label at a time. Hopefully, having the entire script readable by google and yahoo will cause it to pop up high in the search ranking.

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DNA-Specific (But Generally Applicable) AMBER With GROMACS 3.3.x: Installation And Notes

The following is the full procedure for installing the AMBER force field port for GROMACS (AMBER-in-GROMACS, AMBER-with-GROMACS, AMBER-on-GROMACS, whatever you want to call it) developed by Eric Sorin at California State University, Long Beach, providing a bit more depth in the installation process (specifically for GROMACS 3.3.x) and a few modified GROMACS files.

As brief background, AMBER (Assisted Model Building and Energy Refinement) is one of THE dominant molecular mechanics/molecular dynamics (MM/MD) force fields used today in biochemical simulations. The motivation for this page (my installing AMBER for use in GROMACS) stems from the current Nanorex focus on Structural DNA Nanotechnology (SDN) modeling, for which we’re working on a reduced model force field for large-structure energy minimizations and, importantly, integrating the GROMACS MM/MD package for use via our CAD interface. You can read more about this in the poster presented at FNANO08 this past April. As a force field validated for DNA simulations, AMBER meets our needs of performing atomistic simulations on DNA nanostructures. While NAMD is also a possibility for DNA simulations, GROMACS meets Nanorex’s open source needs.

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Lifeboat Foundation Nanotechnology and Chemistry Advisory Board Membership Note

“As Wednesday morning dawned, northern Norway was hit with an impact comparable to the atomic bomb used on Hiroshima.” – Nina Ldemel,, June 9, 2006.

norway meteor

The old joke is that “the difference between mathematicians and physicists is that mathematicians stare at their own shoes, while physicists stare at other people’s shoes.” Given how insignificant much of the activities of humanity are compared to how much time major media outlets spend on them (note that I post this in the wake of having to listen to stories about Jamie Lynn Spears), it is perhaps not surprising that I didn’t find out about the above news story from any US media source, instead having to rely on my international news searches as part of my monthly research for astronomy-related news for the Syracuse Astronomical Society President’s Message.

Ponder the headline for a moment. Norway. Impact. Atomic Bomb. Those of us that prefer the freezing cold outdoors with our scopes to crowded indoors with beverages already know that debris falls into our atmosphere all the time. If you believe the United States Geological Survey (USGS) estimate (and I see no reason not to), 1,000 tons of dust and debris fall to earth from space every year. A meteor shower is a predictable time to see matter speeding into our atmosphere and streaking across our field of view (which, of course, isn’t exactly correct, as the Earth is actually speeding into a debris field during meteor showers), but you can be sure to see 1 to 5 meteors an hour by simply being outside any night. So, ponder the following. What if that Norway meteor had been 6 hours later and 20 degrees lower latitude (that’s New York City, where I’m writing this post from). Or, perhaps, any other major populated area. Or, perhaps, just a location with a large enough population that a news story like the Norway impact would have made it beyond local headlines and a few internet news services. There are plenty of places to choose from if this map of human civilization is any indicator.

earth at night

From Astronomy Picture of the Day. Click on the image for a larger size.

A random yet relevant quote from the movie Armageddon, 1998:

President: Dan, we didn’t see this thing coming?

Truman: Well, our object collision budget’s about a million dollars. That allows us to track about 3% of the sky, and begging your pardon sir, but it’s a big-ass sky.

For the most part, humanity hasn’t developed far enough where the potential catastrophes from “above” (hence the shoe-staring humor) are of as much concern as the potential disruptions “on the ground.” I suppose, in the universal scheme of things, a species that hasn’t progressed to the point that it’s truly aware of its place in the universe and cognizant of the need to worry about the whole picture simply hasn’t developed far enough where it will make a dent anywhere else in the cosmos, is a long way from being consequential, and, therefore, not yet worth any another, sufficiently-developed species’ attention. We’ll have matured as a species when we concern ourselves more with our persistence beyond the statistical averages of stellar and cosmic phenomena than with resource squabbles here on Earth.


Existential risk is a risk that is both global and terminal. Nick Bostrom defines an existential risk as a risk “where an adverse outcome would either annihilate Earth-originating intelligent life or permanently and drastically curtail its potential.”

Fortunately, small groups of people have at least begun to think about, and plan for, existential risks such as the “global killers” of rock and ice that couldn’t care less about the ongoing Writers’ Strike, the Presidential Primaries, or Global Warming. The stuff from “on high” isn’t our fault, so I think it something worth worrying about more than those things we do to ourselves, if for no other reason than intra-species conflict IS our collective fault and, as long as EVERYTHING is connected and EVERYTHING matters, someone can always connect the dots with James Burke-ian clarity to show that we somehow did it to ourselves.


With all that Christmas cheer in mind, I’m pleased to report my addition (click here for my snappy bio) to the Advisory Board of the Lifeboat Foundation, one of the precious few organizations that is looking up and looking around in efforts to guarantee the persistence of our species. I’ve been acquainted with Lifeboat by way of their financial director, Michael Anissimov, for quite some time, both through his excellent Accelerating Future blog and through some lively interviews, including one at Podcasting The Singularity and another at RU SiriusNeofiles Show. Of course, my addition is to the Nanotech and Chemistry Boards, nothing astrophysics-related, but what the hey…

From the Lifeboat Foundation website:

The Lifeboat Foundation is a nonprofit nongovernmental organization dedicated to encouraging scientific advancements while helping humanity survive existential risks and possible misuse of increasingly powerful technologies, including genetic engineering, nanotechnology, and robotics/AI, as we move towards a technological singularity.

Lifeboat Foundation is pursuing a variety of options, including helping to accelerate the development of technologies to defend humanity, including new methods to combat viruses (such as RNA interference and new vaccine methods), effective nanotechnological defensive strategies, and even self-sustaining space colonies in case the other defensive strategies fail.

We believe that, in some situations, it might be feasible to relinquish technological capacity in the public interest (for example, we are against the U.S. government posting the recipe for the 1918 flu virus on the Internet). We have some of the best minds on the planet working on programs to enable our survival. We invite you to join our cause!

And keep your eye on Apophis.

Single-Atom Manipulation And The Chemistry Of Mechanosynthesis Slidecast At

Direct link to the Slidecast is available HERE. Local copy of Slidecast content is available HERE.

I am pleased to report that an abridged version of the talk I gave at the SME Nanosystem Roadmap Conference (containing one set of tooltip work being performed in collaboration with Eric Drexler and a second in collaboration with Robert Freitas and Ralph Merkle) is now available as a slidecast at By way of introduction, I posted about previously when the 2nd Edition of the CRC Handbook of Nanoscience, Engineering, and Technology was published, as the nanoscienceworks site is managed by the handbook publisher, Taylor and Francis. is an information-rich place for nano-researchers (where a biography of your truly is located), publications, and nano-related news aggregated from various sources. Slidecasts are steered PowerPoint presentations with associated audio, all in Flash format for universal playability (I think they’re more generally referred to as screencasts, but they may be new enough that you can call your own label). Unlike a typical research talk, you have time to meditate on verbal content before committing to mp3 format, quite handy when you tend to fly through concepts or find yourself inundated with new research ideas as you walk through the slides and then find yourself jotting notes and leaving long quiet spells in the audio. And if the possibilities of Slidecasts tickle your fancy and you want a thorough range of examples to steal, er, borrow presentation ideas from, I recommend heading over to, whose “About Us” is cohabitated by none other than the good Dr. Deepak Singh.

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