Hi everyone. I have tried to modify the saWithPreAllNoRdc.py script from the PrePot distribution to calculate the structure of a complex using only PRE data. I have the PDBs for both proteins. If I use something like dyn.fix, it doesn't look like the proteins move in space. So, I am currently testing the script with dyn.group in the IVM portion. Is this the correct approach? Should I use a "vector do" command for randomizing velocities?
These proteins likely form a weak-affinity complex, so I only have PRE data (1H Gamma2 values) to model the interaction. Using the dyn.group approach, it looks like the secondary structure and tertiary structure are being perturbed. Has anyone used this script before for only PDBs and PRE data? Additional info: a separate Psf and PDB file are read in for each protein; the Psf and PDB generated for the MTSL-labeled protein is for a 3-conformer model (ALT1, etc). Any feedback would be appreciated! Valerie
