Hi all, I've been getting blocked running minimize/optimize from tinker. The issue is atom types and energy parameters. For small molecules, I can hand check the types and get tinker to complete successfully. However as my molecules get larger (and I'm attempting to automate a screening protocol), by hand isn't going to scale.
I've tried several approaches to parsing a file and getting types set. As examples, I've used obabel to convert a PDB to a TXYZ which should correctly target the atom types for the MM2 parameter set. I've also used MolKit and Pybabel to attempt the same thing. It's frustrating that I can load the molecule into Avogadro or Ghemical and have no issues at all with energy minimization. 1. Is there an option to tinker programs to tell me exactly where the issue is? 2. Does anyone have a reliable atom type setting script? 3. Is there a force field set I should be using besides MM2? Thanks in advance for any assistance... britt
