Thanks again. I agree that "Physics where you want it" will be helpful here. I'm having a problem using matchGapped in MMB. The last lines of the output are: /home/flores/svn/RNAToolbox/trunk/src/BiopolymerClass.cpp:372 About to optimize chain A using ObservedPointFitter /usr/local/Installer.2_8.Cen...

Thanks for the quick replies, and apologies for my own delay. What I'm looking to do is simulate a large protein using various levels of resolution in the structure and energy function. The protein is a homomultimer, each subunit of which contains two domains joined by a flexible linker. As a starti...

Hi, I am trying to get a handle on what happens when a PDB file is read using 'protein'. In ExampleLoadPDB2.cpp, immediately after State state = system.getDefaultState(); I added: protein.writePdb(state,std::cout); return 0; I thought that this should print the input structure, modulo rigid transfor...