Re: [AMBER] Mapping back the original PDB numbering and chain IDs when analysing Amber trajectories

From: Daniel Roe <>
Date: Wed, 9 Nov 2016 13:57:59 -0500

On Wed, Nov 9, 2016 at 1:32 PM, David A Case <> wrote:
> We offer a partial solution: First, use the add_pdb program (or better,
> the addPDB action in parmed) to put the information from the original pdb
> file into the prmtop file. Then, you can use addpdb with the -ext flag
> to create a pdb file with the original information. Or, you can use the
> outPDB action in parmed with the norenumber option.
> This is a workable solution for a single snapshot; it is less helpful to
> analyze an entire trajectory. (VMD doesn't know how to interpret the
> "extra" in the prmtop file.

FYI, cpptraj will read and use the extra PDB info in an Amber topology
file added by parmed's 'addPDB', so e.g. if you write out a PDB you
should have the original residue numbering, chain IDs, etc.


> Others on the list may have their own workflows that address this problem.
> ...dac
> _______________________________________________
> AMBER mailing list

Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
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Received on Wed Nov 09 2016 - 11:00:03 PST
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