> > > > > prot = loadpdb /home/kkm7r/pdb/cyt.pdb
> > > > Loading PDB file: /home/kkm7r/pdb/cyt.pdb
> > > > +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> > > > +---Tried to superimpose torsions for: *-C4D-ND-*
> > > > +--- With Sp2 - Sp0
> > > > +--- Sp0 probably means a new atom type is involved
> > > > +--- which needs to be added via addAtomTypes
Have you addressed the adding of new atom types yet? This Sp0
message refers to hybridization types that get defined in the
leaprc - only leap uses these (they don't get into the prmtop).
If you are using a leaprc in another directory (standard loading
procedure), copy it to your working directory and add the
missing types.
Bill
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Received on Sat Dec 11 2010 - 11:30:05 PST
