Guys, Not sure if I should put this here, I don't know if anyone monitors the molmodel forum.. I want to be able to make posttranslational modifications to amino acids in a peptide. For example, let's say I have some sort of non beta branched "stub" amino acid, and I want to add arbitrary atoms to r...

Hi Sherm, Of course! The whole point of the private implementation is to include the headers in the .cpp rather than in the header. This is starting to make sense. I did as suggested and committed my changes. It seems to work in MMB as well. At least, the potential energy for the total system is dif...

Regarding the Body::Rigid(int) problem, yes, you did fix that. I had updated the molmodel source and headers, but neglected the test directories. I realized my mistake, which is why I deleted my comments on the forum. Sorry for the confusion. I'm a bit curious as to how this bug could have originate...

with regard to getRep(), I made that private again. I also implemented calcPotentialEnergy as suggested. I had tried some variants of this before, actually: 316 public: 317 318 //class DuMMForceFieldSubsystemRep& updRep(); 319 //const DuMMForceFieldSubsystemRep& getRep() const; 320 Real calcPotentia...

Hi Sherm, I have another question. I'm trying to access this function: Real calcPotentialEnergy(const State& state) const; .. which is defined in DuMMForceFieldSubsystemRep.h . A private implemention, of course, which I don't fully understand. At any rate, I tried to declare it as a member of DuMMFo...

* the rest of this message is cancelled, saw the issue now.

right, I suspect leftover crap is the issue.

* the rest of this message is cancelled, saw the issue now.

Hi Sherm, Thanks for your work. I am using the simbody I downloaded from trunk when I saw you a couple of weeks ago (looks like 3.6). Hopefully that's ok? I updated molmodel as instructed but the error is still the same. But this may be a peculiarity of my home laptop, since it doesn't happen at wor...

Hi Sherm, I was able to fix this (also removed the FORCE keyword). However this does not seem to have been the problem (error messages unchanged, see below.) I verified that SimTK_INSTALL_DIR is correct: SimTK_INSTALL_DIR /usr/local/SimTK (also tried /usr/local/SimTK/lib) SimTK_INSTALL_PREFIX /usr/l...

Guys (Sherm?), I'm having trouble building molmodel on a macbook pro running OSX 10.9.5 . This is not the laptop I had in Sherm's office. The errors go like: samuel-floress-macbook-pro-2:build Sam$ make -j8 Linking CXX shared library ../libSimTKmolmodel.dylib Undefined symbols for architecture x86_6...