caDNAo extension to predict origami shapes

[Tom]

http://web.mit.edu/newsoffice/2011/dna-origami-0427.html

I'm not sure what the long term plan is with respect to NE1 and DNA,
but it looks like it would be very difficult to catch up now. BTW, are
there any long term plans for new versions of NE1.

Best,

Tom

[Bryan Bishop]

On Mon, May 2, 2011 at 7:22 PM, Tom Moore wrote:

I'm not sure what the long term plan is with respect to NE1 and DNA,
but it looks like it would be very difficult to catch up now.

Why would you want to catch up? Both code bases are open source. Just integrate the code... no big deal.

As for releases: there are no active developers writing code for NE-1 right now. I am just hanging out here doing maintenance work once in a while because NE-1 shouldn't die into oblivion.

 
- Bryan
http://heybryan.org/
1 512 203 0507

[Tom]

Right, catch up was a poor choice of phrasing. I meant it in the since of developing a user base, not technology wise.

Tom

[Tom]

Maybe the best way to ensure NE1 doesn't die in oblivion is to give it some more utility. I have used a lot of chemistry and nano-scale modeling programs. I think NE1 has one of the best UIs out there. It may be interesting to hook this interface into some other research grade calculator/simulator.

Previous version of NE1 were going to use PCGAMESS (now Firefly), but this was removed when the focus switched to DNA. It might not be that hard to but it back in. Gabedit serves as a gui for quantum chemistry programs (http://gabedit.sourceforge.net/), but building structures in it is awful.

Of course there is the GROMACS possibility. One of the great features of GROMACS teamed with NE1 would be GROMACS' ability to apply external forces on groups of atoms and NE1 jigs. There is a large user base of people that are interested in using gmx but have a lot of trouble with the lack of a gui. I get a couple of new emails a week from them.

There are also a few python modules that are research-grade such as Atomistic Simulation Environment:
(https://wiki.fysik.dtu.dk/ase/)

Please let me know if there is any interest in this direction.

Tom
 

On Mon, May 2, 2011 at 11:50 PM, Bryan Bishop <kan...@gmail.com> wrote:

[Thomas Fitzsimmons]

Hi Tom,

Tom <moor...@gmail.com> writes:

[...]

> Of course there is the GROMACS possibility. One of the great features of GROMACS teamed with NE1 would be GROMACS' ability to apply external forces on
> groups of atoms and NE1 jigs. There is a large user base of people that are interested in using gmx but have a lot of trouble with the lack of a gui. I get
> a couple of new emails a week from them.

When I packaged NE1 for Fedora I added a patch to automatically
configure GROMACS paths, so at least some support is already there.
Have you tried using NE1 as it currently exists as a front-end to
GROMACS?

Thomas

[Tom]

Hi Tom,

Not exactly. I believe GROMACS has been implemented to some extent already to minimize the energy on large DNA structures. Mark Sims would be better to fill us in on this, but I know you can select minimize energy using gmx and the ND-1 force field. There is also the ability to check AMBER atom types for using the AMBER force field (good for DNA). It seems a lot is already there to do something with gmx. If we could expand the simulation features of NE1 to use gmx, and include a force field editor, NE1 could become a very useful basic gmx interface that we could build on in the future.

Tom