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.
Presumably you also specified a one-letter code in restyp.lib?
> 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.
Exactly - where parameters are not supplied, it guesses, using the current geometry as the input.
> 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 > > > At this point that error means absolutely nothing to me.
You're not expected to understand what these errors mean. ;) Assertion failures mean a bug in the code. Can you please put your input files (script, template, and modified topology/parameters) in a zip or .tar.gz file, and send it to me, so that I can reproduce (and fix!) your patching problem and this fatal error?
> The entries in the parm.lib file are often redundant for many entries. Are > the columns described somewhere?
You mean par.lib? That's just a CHARMM parameter file. It's documented, along with the top.lib, at www.charmm.org.
> Do I need to have explicit entries in the parm file for an atom that I hope > to delete?
I don't think so, but if you can send me your example, I'll take a look.
> I have not deciphered how to designate bond order in either the RESI entry > or the PRES entry lines. How does one specify bond order?
The CHARMM forcefield has no concept of bond order, so there is no way to specify it in the topology file. What effect do you want bond order to have?
Ben Webb, Modeller Caretaker