AMBER Archive (2002)

Subject: Re: SHAKE (actually: new atom types)

From: Bill Ross (photoriot_at_yahoo.com)
Date: Mon Jun 24 2002 - 14:22:02 CDT

> when loading a pdb file (containing the membrane)
> into xleap i get a funny message:
 
+---Tried to superimpose torsions for: *-C9-O5-*
+--- With Sp2 - Sp0
+---Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported

Once a type is defined in the .lib file, it needs
to be supported in 2 places: the force field
(parm.dat), which defines the type in energy-related
terms, and the leap atom types (see addAtomTypes),
where hybridization is defined. Either the C9 or O5
atom type has undefined hybridization. The
hybridization info is used when placing missing atoms;
it also comes into play when minimizing selected
atoms in leap when energy parameters are missing.
(Note that leap's minimization does not include
electrostatic or vdw, so is purely for convenience
during model building.)

Bill Ross

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