Toyoma san Konbanwa! MD of nucleic acids is quite complex, you would need to add counterions and water. Even then, MMB is not really an MD code. You might want to try nucleotide conformers. These will improve the backbone structure. should be available in versions 3 and 4, download that and then loo...

In the unpaired region there are not restraints at all, so the residues can do as they wish. I would start by adding collision detecting spheres, use the AllHeavyAtomSterics scheme. For the helical parts, you will get better quality if you use NtCs, if you don't know you can assume you need AA00. I ...

Hi Nicole, Great application! Not sure which version of MMB you are using. Assuming it is a recent release, you can follow exercise 1B to apply NtCs: http://pe1.scilifelab.se/MMB-annex/MMB.3_4.tutorial.pdf To improve the helical structure I very strongly recommend adding Jiri Cerny's Nucleotide Conf...

super quick update.. the trunk version does actually appear to still read in the old asterisk-named atoms. Really it shouldn't, but there it is.

one more thing -- why are you adding hydrogens? MMB structures have hydrogens already.

Sam

Hi Michael, Thanks for raising this issue. Since birth molmodel has been naming the ribose atoms correctly using an apostrophe (e.g. C5') for the FIRST residue. However for reasons unknown it goes with stars for all subsequent residues (e.g. C5*). The latter is not consistent with PDB rules, so it i...

Hi Daniel, Absolutely! This is very doable. As I understand, you already have a complex of the RNA and protein together, but you want to make a mutation. So what I would do is prepare an input PDB file with your protein and RNA, you can call it e.g. last.1.pdb. Then in your commands.dat you would ca...

Hi Daniel, Exercise 0 is just to make sure you installed everything and know how to invoke MMB and look at the output. It forms only one base pair and the steric clashes are prevented with some cheap collision detecting spheres, so it is not very physically realistic. It takes a little practice to l...

Hi Sherwood,

Sorry I didn't get a notification of your post. Did we talk about this by phone? You would need to specify the base pairs or any NtC's. There is a simple hairpin example in the tutorial guide that can help. We can also discuss again by phone.

Sam

Guys, I am using computeNeighborListVoxelHash to find all the neighbors of a list of specific atoms, in the system. Basically I want to specify a short stretch of viral DNA, and find all atoms (in this case, other DNA atoms) nearby. I am not sure I am using this function in the most efficient way, a...

Another alternative is to install Docker for Windows. I now have a docker MMB image, called:

samuelflores/mmb-ubuntu

I have not tried docker for windows but don't see why this would not be a solution.