Re: AMBER: Antechamber & Ptraj/Rdparm

From: Bill Ross <>
Date: Thu, 1 Jan 2004 14:26:55 -0800 (PST)

> Loading PDB file: ./60-new.pdb
> Unknown residue: NO_ number: 0 type: Terminal/last
> But 60-new.pdb is the one I used prmtop & inpcrd files to
> get. I still cannot load it. Did I miss anything?

When you created the prmtop & inpcrd files, how was your
NO_ residue defined? Did you load a template file you had
created earlier? If so, you would need to load that file
again before loading the pdb, so that the residue in the
pdb would match the loaded template.

If you did not create a template file for NO_, I suggest
doing so now. All residues need templates for proper loading
from pdb, and it is easier to save the templates to a file
and reload them than to create the template manually every
time it is needed. The templates contain

  ** bonds
  ** atom types
  ** charges
  ** default 'connect' atoms

in addition to atom names. You might also want to have atom
names that follow the pdb convention - although these may
work ok, there may be some software that has a problem with
the non-standard '_' character.

> Created a new atom named: HO_3 within residue: .R<NO_ 1>
> Created a new atom named: C_3 within residue: .R<NO_ 1>

Bill Ross

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Received on Wed Jan 14 2004 - 15:53:13 PST
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