Starr Hazard wrote: > I have created a RESI entry in top_heav.lib for a ligand of interest to me. > When run without attempting to patch anything the RESI is accepted just > fine and > models are made with the appropriate ligand in an appropriate location. ... > I created a PRES entry based on the disulfide example. ... > When I perform a test run of the code patch.py from the on-line manual > (where I have added > "env.io.hetatm=true" to read the ligand). The program appears to run but > the log file shows numerous entries of this sort > > r_stere_607W > Cannot find parms in parm file > Then remarks indicate that it has "added" some parms; so it gets past some > instances where explicit information has not been supplied. > > > It gets to a particular dihedral involving an atom that is supposed to be > deleted by the patch ( see line above- 'DELE ATOM 2:O32' is the line in > top.heav.lib; this is the aldehyde oxygen) and stops. > > The final line reads simply: > > FATAL error: assertion nbndpf < mbndpf failed in r_stereo.F90, line 608
Just to follow up on this for the list: there are two bugs in Modeller exposed by this example: an off-by-one error causing the assertion to pop up when it shouldn't, and a bug in the handling of patch atoms limiting the names to 4 characters (so that atom "2:O32" is not deleted, but instead the deletion of "2:O3" is attempted). Both have been fixed in the 9v2 release.
Ben Webb, Modeller Caretaker