[Chimera-users] Chimera: Amber to PDB

Eric Pettersen pett at cgl.ucsf.edu
Mon Aug 27 13:59:18 PDT 2018

Hi Boris,
	Well, not directly.  If you run the AddCharge tool (or ‘addcharge’ command), which will in turn add hydrogens if any are missing, then the “Amber name” of the residue is computed and put into the ‘amberName’ attribute of each residue.  So, if you then run the Python script below (simply by opening it with File→Open or the “open” command), then the regular name of the residue will be overwritten with the amberName attribute and if you then save a PDB file, the residue names will use the Amber convention.


	Eric Pettersen
	UCSF Computer Graphics Lab

> On Aug 27, 2018, at 2:00 AM, Boris TOUZEAU <boris.touzeau at gmail.com> wrote:
> Hi,
> I am Boris TOUZEAU, actually a PhD student at the National Taiwanese University (NTU) based in Taipei. 
> I had a question about chimera; Is it possible to output pdb files having amber residues naming convention instead of pdb residues naming convention ? I saw it was possible to do it for the atoms (ligands) but I would be more interested to do it for residues.
> Best wishes,
>     Boris TOUZEAU
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