Interactive molecular dynamics in SAMSON: Docking example

[CantFindaName9999999]

any idea about system requirements (OS, processor, memory)?

[StephaneRedon]

The example above runs on my laptop: a DELL Inspiron M6300 with 4GB of RAM and an Intel X7900 dual core 2.8GHz CPU, running Vista. SAMSON currently runs on both Windows and Linux, but we will also try to release a Mac version.

[CantFindaName9999999]

thanks stephane. wonder if i could ask 2 further questions --

* are the specs you mention a minimum? how limited would the system be, for instance with 1GB RAM or 2GB RAM?

* does the graphics code use openGL or directX?

[StephaneRedon]

We have not tested for minimum specs, but it basically depends on the size of the system you want to simulate (for memory specs), and the number of degrees of freedom you want to be able to simulate at the same time, as well as the force-field you want (for CPU specs). You can run more complex systems than the one above with only 1GB.

The graphics code uses pure OpenGL for now.

[CantFindaName9999999]

cool...

i wonder -- is SAMSON opensource? is it actively maintained? in any event, can't see where to find it online. any suggestions?

also, just curious -- what are the other programs for IMD which you refer to? (i see a movie here for "zodiac", don't know anything about it)

[StephaneRedon]

SAMSON is currently being developed by the NANO-D group at INRIA (link above in the video information), and should be released in Spring 2009. It will have an open architecture, with a SDK to allow users to add plug-ins to the SAMSON platform (for example to add custom force fields, models, solvers, etc.).

I was referring to NAMD+VMD, developed in the Schulten group at UIUC.

[vdubmerc3]

Thanks for replying! I have tried autodock, but they want you to download some linux-like operating system and I didn't work on my computer. I'm trying IMD, and I hope it works.

Is SAMSON as easy as it looks on this video? It looks like all you have to do is drag your compound near a protein to dock. Is there any algorithms you need to do?

[StephaneRedon]

Sorry for the delay. Yes you only have to drag the ligand around and dock it where and how you want - there are no algorithms that you have to run at the moment (everything is interactive for now, but this might change later if necessary). Note that it helps to have an 'a priori' idea of where docking might occur though, so it might be useful to run complementary algorithms which will attempt to predict a docking configuration, which will be later edited in SAMSON.

[vdubmerc3]

Very nice. Are there any other docking programs like SAMSON. I'm only asking because SAMSON won't be released until spring 2009, and I really need to do some molecular docking for a research project.

[StephaneRedon]

Thanks! Other programs exist for automated docking (e.g. AutoDock), or for interactive molecular dynamics (e.g. IMD), which you might be able to use to dock molecules.