Re: AMBER: Problem taking the PDB to the Amber coordinates for calculations

From: David A. Case <>
Date: Tue, 7 Mar 2006 11:47:30 -0800

On Tue, Mar 07, 2006, Brian Stupi wrote:
> > model = loadpdb “ADENandTHYM_c_TER_c_mod2.pdb”
> Load PDB files: ./ADENandTHYM_c_TER_c_mod2.pdb
> Created a new atom named: H within residue: .R<DT5 4>
> Created a new atom named: H within residue: .R<DT 8 >


You have to make sure that the atom names and residue contents in your
PDB file match those in the Amber library. In some cases, this just means
editing the PDB file (particularly for hydrogen atom names.) In some cases,
what is in a pdb file may not have the same chemistry as standard residues
(what is called "A" or "ADE" in a pdb file might not correspond to the residue
of the same name in the Amber database.) Then you have to either modify the
input pdb file, or create a new residue in LEaP that matches what is in the
pdb file.

...good luck...dac

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Mar 12 2006 - 06:10:13 PST
Custom Search