We're trying to dock two proteins. One of them has a bound acetate ion. We created the centroid & full atom params files for the acetate, residue name ACT, using the params generation utility. We specified the location of the params files in the flags script using the -extra_res flags. The file locations are correct. We modified the flags file from one that ran sucessfully before, so we're pretty sure that's correct. Nonetheless, the docking run crashes quickly with the message "unrecognized aa ACT". Acetate does have a C=O and an OXT, which may be causing problems. How do we work around this?
Can you attach the params file you generated, along with the snippet of the PDB containing the offending residue? (rename to *.txt to get the forum to accept it.)