Re: [AMBER] Creating topology files for protein-ligand complex

From: case <>
Date: Wed, 16 Jun 2010 22:51:26 -0400

On Tue, Jun 15, 2010, Heather Condurso wrote:

> > loadoff ye1.lib
> Loading library: ./ye1.lib
> > complex = loadpdb 2NP9S_trunc.pdb
> Loading PDB file: ./2NP9S_trunc.pdb
> Unknown residue: YE1 number: 423 type: Terminal/beginning

Residue names are case sensitive. In "ye1.lib" the residue name is "ye1",
whereas in the pdb file it is "YE1".

> Unknown residue: OXY number: 424 type: Nonterminal

You also have a residue in the pdb called "OXY" (looks like dioxygen). You
will need to make a library file for this as well.


AMBER mailing list
Received on Wed Jun 16 2010 - 20:00:04 PDT
Custom Search