Re: [modeller_usage] wrong topology for the ligand?
To:
Subject: Re: [modeller_usage] wrong topology for the ligand?
From: Cvetan Stojkoski <>
Date: Wed, 17 Nov 2004 11:06:40 +1030
Organization: University of Adelaide
On Tue, 16 Nov 2004 14:07:48 -0800
Modeller Caretaker <> 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