Hi, I'm just getting familiar with IMP, looks like a fabulous peace of code! Trying the example in https://integrativemodeling.org/2.4.0/doc/tutorial/kinematics_rrt.html appears to work as intended, however, there are a few questions:
1. I get a warning: WARNING Could not determine CHARMM atom type for atom "HET: C1 " in residue #475 "NAG" so I wonder is there a way to include the sugar topology/parameters in some way - I do seem to recall that the CHARMM FF does have parameters for sugars, at least those found commonly in the PDB.
2. I also get WARNING No CHARMM parameters found for angle S-S-CT2 is this not an interaction that should be there in any CHARMM protein FF?
3. When I include any atom and the corresponding residue into both linker.txt and conect_chains.txt then I get: ERROR: IMP currently does not support switching of parents in a kinematic tree when I do not include the atom numbers (of the corresponding SG atoms) into conect_chains.txt but leave the residues that contain these atoms in linker.txt then it seems to work. What I wonder is: is the tool smart enough to figure out which CYS are S-S bonded on it's own, and account for that during optimization? If not, is there any other way to use S-S bonded cysteins in the linker?
4. I haven't tried out compiling from source yet ... but I'd really like to see whether CUDA gives me any speedup ... is it anywhere documented which parts of the code or which algorithms run on GPU in the current version of IMP?
thanks for any help! regards Michael