Re: [AMBER] Avoiding pdb4amber renumbering

From: David A Case <>
Date: Tue, 23 Jan 2018 15:14:22 -0500

On Tue, Jan 23, 2018, Sundar wrote:
> I am new to Amber and I have question on how to avoid atom renumbering when
> using pdb4amber.
> I couldn't find a clear answer to this in the amber mailing list archives.
> pdb4amber forces protein's atom numbering to start from 1. I certainly
> don't want that.

As its name implies, "pdb4amber" is designed to prepare pdb files for *Amber*,
which internally always numbers atoms and residues starting at 1. It creates
a "renum" file than can be used to map the original numbering scheme to the new

If you don't want the renumbering to occur, then it seems likely(?) that you are
planning to use the output for something else than feeding to Amber.

So: there is no option to avoid the renumbering, since that is in many ways
crucial to what pdb4amber is designed to do. There are a number of ways
to reference the "original" residue numbers: see, e.g. the addPdb action
in parmed, and the -ext flag in ambpdb.


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Received on Tue Jan 23 2018 - 12:30:03 PST
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