thanks for your kind words. I guess the scrubber is pretty nice but I am not sure it is so novel. It is effectively potential rescaling and simulated annealing. In any case numerical instability has not been an issue. I agree it sounds violent but the forces are not large and sudden enought to force...

nucleicAcidDuplex will work with the force field turned on, but you have to do two things: 1. Make sure the base pairing forces are strong enough. You can increase them by 100 or 1000x just to test. 2. Make sure the MD forces are turned off for the template. I am afraid you will probably have to pla...

Sorry I lost track of this thread. It is not clear to me what you are doing. Homology modeling should use the alignmentForces command. If you have issued setDefaultMDParameters this turns on the Amber99 potential which you have to be careful about, because it can repel all the atoms and counter what...

How did it go?

Thanks for pointing out the library issue. What version of MMB are you using? Possibly it is the tutorial which is wrong. I will have to make sure it is telling people to set LD_LIBRARY_PATH the right way.

sam

yes, the inserted residues are treated like any other residues. So you can apply base pairing forces to them. the spiderwebby effect is probably a viewer issue. If your initial structure has clashes, your viewer will probably get the bond network wrong. In VMD, I usually load a fully extended , ster...

I should have mentioned this. Oddly, this variable is not used at all in Simbody's CMakeLists: -bash-4.1$ grep BUILD_SHARED CMakeCache.txt -bash-4.1$ grep BUILD_SHARED ../CMakeLists.txt -bash-4.1$ I did manage to build on another server this time, and then move the files to the server of interest, b...

Neither of these worked.

Hi Christopher, I append my CMakeCache.txt in case that is useful. I tried setting #define _GLIBCXX_USE_CXX11_ABI 0 in the problem files and in the top level SimTK common files, but all that seemed to do is shift the problem around. Anyway I believe I ultimately have to compile to the c++11 standard...

Hi Christopher, I tried it both ways. CMAKE_CXX_FLAGS -std=c++11 -stdlib=libc++ gave me an error: g++: error: unrecognized command line option ‘-stdlib=libc++’ leaving it blank: CMAKE_CXX_FLAGS again gave me what look like c++11 related errors: [ 8%] Building CXX object SimTKcommon/tests/CMakeFiles/...

Hi Christopher, Thanks, that got me further! I was able to build the libraries without further errors. However I could not build the tests. I got what look like c++11 errors, appended below. But I believe I am setting the c++11 flags correctly. In a probably unrelated issue, I also can't compile mol...