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

From: David A Case <>
Date: Wed, 9 Nov 2016 13:32:20 -0500

On Wed, Nov 09, 2016, Eric Lang wrote:
> I am working with a heptameric protein and during the preparation of the
> system in Amber, all the residues are renumbered in a sequential order and
> the chain IDs are removed.

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.

Others on the list may have their own workflows that address this problem.


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Received on Wed Nov 09 2016 - 11:00:02 PST
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