I am building on OS 10.12 Sierra.

thanks

sam

Guys, I am getting a puzzling warning when building the latest release of simbody. Actually it only occurs when building examples, but since I am having problems downstream I think this needs to be addressed. The warning is below. Any advice? Thanks Sam In file included from /Users/Sam/github/simbod...

Sorry I seem to be missing these messages. 1. You can expect unphysical results if parts of your molecule are flexible and physics is not turned on, or is not turned on for enough of the nearby residues. For homology modeling you have to be very careful to keep the MD forces turned OFF for the templ...

Hi Xiong An, I made a few modifications to your script. Assuming you are using the latest build, it will be easier to work this way. First, you can just issue "mobilizer Rigid" to rigidify everything, and then set 51-69 back to being flexible. You can use nucleicAcidDuplex to make base pairs in a do...

I would use "Default" rather than "Free". Free confers 6 degrees of freedom (DOFs) for each bond. Default makes most bonds either Torsion (1 DOF) or Rigid (0 DOF). Rigid is for groups like phenols, or the peptide bond, that MMB prefers to treat as though they had no internal DOFs. Anyway, Free costs...

Oh sorry by threading I meant homology modeling. Where did you see the term "threading"? MMB was the first homology modeling method for RNA. You can read about it here: http://psb.stanford.edu/psb-online/proceedings/psb10/flores.pdf Morphing is just finding a trajectory connecting two known structur...

In this case the complexes AB and CD are highly similar. So constraining A to B should give almost the same result as not constraining -- the differences should be on the order of tenths of Ångströms (there will be other situations in which this is not the case, hence the need for constraints). Howe...

Guys, Is there an incompatibility between Constraint::Weld and LocalEnergyMinimizer::minimizeEnergy ? I create one complex comprising proteins A and B, which are constrained to each other (I want them to stay together, moving as a single rigid body) and then apply springs to pull them onto another c...

Hi Kamlesh, I am not sure I would recommend this approach. You can eventually get this to fold but it will be prone to kinetic traps. We got out of those using the Scrubber as described in the RNA and TCBB paper, but it took some patience. At the time it made sense because there was plenty of low-gr...

Hi Crystal, I just realized I didn't answer you earlier. Bug me if that happens! Before I tell you the answer, I intended for MMB to be as easy to use, and as flexible with respect to the structural and other data it takes, as possible. I also intended for MMB not to think too much for you, as guess...