On Mon, May 16, 2011, Paul Rigor wrote:
> I was using chimera (Windows/Linux) and then compiled ambertools (Linux)
> directly for preparing a ligand for docking. However, I've run into
> problems adding partial charges. Below is a detailed run from the Chimera
> log along with a not-so-verbose error message. Any help is appreciated. And
> attached is the molecule I'm working with. I've already attached hydrogens
> to the attached molecule through 'reduce'.
??? It doesn't appear that any hydrogens have been added, at least not in
the file lycopene_h.pdb. Unless lycopene is in reduced HETATM database, it
won't know how to add hydrogens to it. Be sure you have a good geometry and
all needed hydrogens before calling sqm.
> Warning: the assigned bond types may be wrong, please :
> (1) double check the structure (the connectivity) and/or
> (2) adjust atom valence penalty parameters in APS.DAT, and/or
> (3) increase PSCUTOFF in define.h and recompile bondtype.c
> Be cautious, use a large value of PSCUTOFF (>100) will significantly
> increase the computation time
This is kind of a misleading message: the error is almost always in the
input file (i.e. option (1)), and I have never personally seen options (2)
and (3) to be needed or helpful.
....dac
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Received on Mon May 16 2011 - 17:30:02 PDT
