AMBER Archive (2006)

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

From: David A. Case (case_at_scripps.edu)
Date: Tue Mar 07 2006 - 13:47:30 CST

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 >

...etc

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

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