Re: [modeller_usage] wrong topology for the ligand?

On Tue, 16 Nov 2004 14:07:48 -0800 Modeller Caretaker modeller-care@salilab.org wrote:

> Alicia's reply is largely correct. Modeller writes only xyz information > into output PDBs, and no connection data; this is why viewing packages > have to guess at the connectivity and sometimes get it wrong. Modeller > uses the CHARMM (not CHARMm) 22 parameter set, and the coverage of > residues other than aminoacids is rather sparse.

You could use a program like X-PLOR or CNS to build a protein structure file (psf) from your pdb and topology/parameter files. You can then display your psf file in programs such as VMD with correct connectivities.

Cvetan