What operating system are you on? I have just fixed this bug in the 2.11 OSX release. The releases for other operating systems are not yet updated. Turns out part of the problem was that parameters.csv did not contain the parameters for DG, DU, DC, and DA bases, as you intuited. It did have them for...

I would suggest you write a command file according to your best understanding and if it doesn't work immediately, send it to me along with the input PDB file and I will edit it for you. I think I may have already done what you are trying to do WRT force fields, as well. I have a feature called "Phys...

Hi Timothy, MMB will generate residues which span the gap you speak of. Just call : matchGapped somewhere in your command file. Then when you specify the sequence of your protein, include the residues which are missing from the input structure file. MMB will then match the full coordinates of any re...

This is actually not trivial. There are a variety of ways to turn cartesian coordinates read using PDBStructure into internal coordinates in a Biopolymer. The simplest way is to use several "matchDefault .." type methods. But, error accumulates over a sufficiently long chain, if you're not using Sim...

<t><br/> sorry again to be responding to an ancient post.<br/> <br/> this sounds odd. I think you're doing it correctly. If you're still interested, try it again in RNABuilder 2.0 and see if it works.<br/> <br/> the syntax has changed, as I think you're aware. let me know if you need help.<br/> <br/...

<t>sorry, i am only now becoming aware that i was not set up to monitor this forum.<br/> <br/> leontisWesthofInFileName has no equivalent in molmodel. It contains the parameters for the base pairing interactions, which are entirely in RNABuilder.<br/> <br/> For the thermostat, yes, you are making th...

The default in rnabuilder 2.0 is NoseHoover .

Sorry, I am only now becoming aware that I was not set up to receive notifications that someone had posted to the forum!

<r>Hi Vitor,<br/> <br/> Sorry, I just now saw this. I don't understand how your distribution could lack libSimTKlapack.so . I have just updated it a few minutes ago and it's in there for sure. More likely you just need to set your library path as follows (in bash):<br/> <br/> export LD_LIBRARY_PATH=...

<r>You should create a new Custom Force which queries the CompoundSystem for each of its Compounds, then queries each compound for each of its atom indices. Once you have that you can get each atom's body index and its cartesian coordinates. <br/> <br/> When the Force's calcForce method is called it...