> > ** Warning: No sp2 improper torsion term for CG-H1-CG-OH
> > atoms are: C3 H2 C2 O2
> > ** Warning: No sp2 improper torsion term for CG-H1-CG-CG
> > atoms are: C3 H2 C2 C1
> > ** Warning: No sp2 improper torsion term for CG-OH-CG-CG
> > atoms are: C3 O2 C2 C1
> > ... and so on
> >
> > What wrong I could do to get this or should I ignore these warnings?
>
> Warnings are not errors: Usually, you can proceed... However in your =20
> case, I do not understand why a sp2 atom is found among the =20
> CG-H1-CG-OH atom types for instance...
>
> more $AMBERHOME/dat/leap/cmd/leaprc.GLYCAM_06
> [...]
> addAtomTypes{
> { "CG" "C" "sp3" }
> { "H1" "H" "sp3" }
> { "OH" "O" "sp3" }
> }
>
> None of these atoms are sp2 but sp3. right ?
I believe what leap is calling sp2 may be any atom with 3 atoms
bonded to it. Does this apply here?
Bill
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Received on Mon Jul 06 2009 - 09:52:14 PDT
