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.