AMBER Archive (2008)

Subject: Re: AMBER: Amber 10 ambpdb bug?

From: David A. Case (case_at_scripps.edu)
Date: Sat May 17 2008 - 23:37:09 CDT

On Sat, May 17, 2008, Sam Danziger wrote:

> Specifically, using the same input files as the Amber 8 ambpdb the
> atoms that were previously called H1,H2,H3 are called 1H,2H,2H.
>
> Is this a bug, or is there something important that I'm overlooking?

It certainly is a bug. Change "2H" at line 564 of ambpdb.f to "3H". I'll
post a bugfix. Thanks for reporting this.

But this just solves a part of the problem, since LEaP also needs to be
updated. A better workaround for now (aside from manually editing the file
that ambpdb puts out) is to remove lines 556-565 of ambpdb.f.

As a side note: the pdb has recently updated its atom nomenclature, especially
for hydrogen atoms: http://remediation.wwpdb.org/downloads.html. The new
scheme used by pdb is much closer (virtually identical) to the internal Amber
nomenclature -- Amber has always followed IUPAC standards, and the pdb is only
now coming up to speed on this.

This means that many of the contortions in codes like ambpdb are no longer
strictly necessary. But in the short term, things will probalby be more
confusing, since we will have to deal with both old and new formats. I'll be
posting soon an updated ambpdb that will output the new pdb atoms names.

...regards...dac

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