Hi there, I'm trying to do implicit solvent simulations of nucleotides, and I'm running into a problem. If I use, for example forcefield = ForceField('amber10.xml', 'amber10_obc.xml') I get the following error. Note that if I use explicit water models with amber10 or amber14, I get no such parameter...

Update - looks like we have a solution here https://simtk.org/plugins/phpBB/viewtopicPhpbb.php?f=359&t=13397&p=38496&start=0&view= The MMB output structures have stars ( * ) instead of apostrophes ( ' ). Replacing the former with the latter seems to create structures which OpenMM is happy with. At l...

Hi Sam - I can't thank you enough for getting back to me with such quick and concise advice! Maybe it's something I would have caught with more experience in the pdb format but alas. I did a search-replace " * " for " ' " and it looks like OpenMM is running the structure now just fine. As to some up...

Sure thing - see enclosed the direct output from MMB for a minimal aptamer - right out of MMB, before any processing (had to change file extension, and sorry about all the simtk remarks. I'm also attaching a version where I had PDBFixer read and write that same file, just to get rid of those remarks).

Thanks for replying! To clarify on the addMissingHydrogens issue, for e.g. at pH=7.0, on ribose carbons it will add protons up to a total of four, keeping two bonds to carbon, for a total of six bonds. It does something similar to some of the backbone atoms as well. (see attached image). https://i.i...

Hi there! I've been using MMB to fold ssDNA for subsequent MD simulation in Tinker with some success. I'm now trying to do the same but with OpenMM, and I'm having difficulty with the MMB --> OpenMM translation. Taking the output structure directly from MMB: firstly, pdbfixer's addHydrogen's method ...

Hi there! I've been using MMB to fold ssDNA for subsequent MD simulation in Tinker with some success (it's a great tool by the way, thanks!). I'm now trying to do the same but with OpenMM, and I'm having difficulty with the MMB --> OpenMM translation. Taking the output structure directly from MMB: f...